Changeset 3386


Ignore:
Timestamp:
May 25, 2007, 5:11:19 PM (16 years ago)
Author:
Martin Svensson
Message:

Moved the FAQs to a part of it's own and changed to use right tags for FAQs

Location:
trunk
Files:
1 added
3 edited
1 moved

Legend:

Unmodified
Added
Removed

  • trunk/build.xml

    r3382 r3386  
    10541054    <mkdir dir="${doc}/docbook/html/userdoc/trashcan"/>
    10551055    <mkdir dir="${doc}/docbook/html/userdoc/webclient"/>
     1056    <mkdir dir="${doc}/docbook/html/faqs" />
    10561057       
    10571058    <mkdir dir="${build}/docbook/html" />

  • trunk/doc/src/docbook/faq/faqs.xml

    r3382 r3386  
    11<?xml version="1.0" encoding="UTF-8"?>
    2 <!DOCTYPE chapter PUBLIC
     2<!DOCTYPE part PUBLIC
    33    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
    44    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
    5     <!--
    6         $Id: faqs.xml 3246 2007-04-16 14:12:23Z martin $
    7        
    8         Copyright (C) Authors contributing to this file.
    9        
    10         This file is part of BASE - BioArray Software Environment.
    11         Available at http://base.thep.lu.se/
    12        
    13         BASE is free software; you can redistribute it and/or
    14         modify it under the terms of the GNU General Public License
    15         as published by the Free Software Foundation; either version 2
    16         of the License, or (at your option) any later version.
    17        
    18         BASE is distributed in the hope that it will be useful,
    19         but WITHOUT ANY WARRANTY; without even the implied warranty of
    20         MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    21         GNU General Public License for more details.
    22        
    23         You should have received a copy of the GNU General Public License
    24         along with this program; if not, write to the Free Software
    25         Foundation, Inc., 59 Temple Place - Suite 330,
    26         Boston, MA  02111-1307, USA.
    27     -->
    28    
    29 <chapter id="faqs">
    30     <?dbhtml dir="faqs"?>
    31     <title>FAQs</title>
    32     <sect1 id="faqs.global">
    33         <title>Frequently Asked Questions</title>
    34         <para/>
    35        
    36        
    37         <sect2 id="faqs.global.reporter">
    38             <title>Reporters related FAQs</title>
    39             <itemizedlist>
    40                
    41                 <listitem>
    42                    
    43                     <para> Q: I can't find my favourite database for annotating Reporters. Can I add my database to
    44                         BASE2 and if so, How should it proceed? </para>
    45                     <para> A: Yes, you can add resources to annotate Reporters. You will need to
    46                         upgrade BASE2 and you may have to contact your system administrator for
    47                         doing so. </para>
    48                     <para>In order to change, remove or add annotations fields attached to
    49                         Reporters, you will need modify the extended-properties.xml file and run a
    50                         BASE update. Please refer to section <xref
    51                             linkend="installation_upgrade.installation"/> for information about both
    52                         processes. Once done with the upgrade, you'll have to defined a new reporter
    53                         import plugin. Instructions can be found under <xref linkend="plugins"/>
    54                     </para>
    55                    
    56                 </listitem>
    57                
    58                 <listitem>
    59                     <para> Q: I have made a mistake while loading my reporters. How can I delete
    60                         them all in one go ? </para>
    61                     <para> A: Please contact your system administrator (maybe in the future use the
    62                         reporter import plugin in delete mode) </para>
    63                     <note>
    64                         <para> Common problem: from the gui, one can only delete elements displayed
    65                             from one given pages so how does one do in order to delete several
    66                             thousands of reporters spread across several pages ? </para>
    67                     </note>
    68                    
    69                 </listitem>
    70                
    71             </itemizedlist>
    72         </sect2>
    73        
    74 
    75         <sect2 id="faqs.global.arraydesign">
    76             <title>ArrayDesign related FAQs</title>
    77             <itemizedlist>
    78                 <listitem>
    79                     <para> Q: I have 20 Affymetrix ArrayDesigns to create from CDF files, is there a
    80                         way to speed-up the creation process ?</para>
    81                     <para> A: Yes, you can use the Affymetrix CDF ArrayDesign plugin to do so. The
    82                         plugin takes as argument as zipped archive containing CDF or CLF or BPMAP
    83                         files. and then creates all ArrayDesign objects in BASE using the CDF files
    84                         basename as Object Name. <note>
    85                             <para> The plugin should be used by Power User or Administrators only.
    86                             </para>
    87                         </note>
    88                     </para>
    89                 </listitem>
    90                
    91                 <listitem>
    92                     <para> Q: What about gal files, is there something similar?</para>
    93                     <para> A: No, not quite yet as things are a bit more complicated. People are
    94                         working on a plugin for help data entry. </para>
    95                 </listitem>
    96                
    97                 <listitem>
    98                     <para> Q: So What it the best way to create an ArrayDesign in BASE2 when
    99                         starting from a gal file ?</para>
    100                     <para> A: Ok, this is a bit more work that with Affymetrix but here is the
    101                         procedure to remember: </para>
    102                     <para>A gal file tells where <guilabel>Reporters</guilabel> have been spotted on
    103                         a Array. So a gal file can be used to do 2 things</para>
    104                     <orderedlist>
    105                         <listitem>
    106                             <para>-Define the features of an Array Design for a non-Affy
    107                                 platform using a <guilabel>Reporter Map importer plugin</guilabel>.</para>
    108                             <para>To do so, after having created an New Array Design, go to the
    109                                 Array Design Item view by clicking on the name of the newly created
    110                                 Array Design</para>
    111                             <para>Click on the <guibutton>Import</guibutton> in the button. If you
    112                                 don't see it, it means that you have not enough priviledges (contact
    113                                 the administrator)</para>
    114                             <para>This starts a plugin whose setting should be 'Reporter map
    115                                 importer' and ' the file format should be 'gal file' (note this has
    116                                 to been defined, if not present, please create the proper reporter
    117                                 map plugin configuration. </para>
    118                             <para>Now, select File and fill in necessary information from the wizard
    119                                 and run the plugin.</para>
    120                             <para>Once done (and if everything went fine), you can see from the
    121                                 Array Design list view that on the Array Design list view page, the
    122                                 <guilabel>Has features</guilabel> entry has been modified and is
    123                                 set to 'Yes (n)' where n indicates the number of spots (features)
    124                                 for this array</para>
    125                             <note>
    126                                 <para>Features can also be loaded from a Genepix gpr file according
    127                                     to a very similar procedure but you will have to create a
    128                                     specific reporter map importer plugin configuration for such
    129                                     file before being able to proceed</para>
    130                             </note>
    131                         </listitem>
    132                         <listitem>
    133                             <para>-Define the <guilabel>Reporters</guilabel> present on this Array
    134                                 Design using <guilabel>Reporter importer plugin</guilabel>. </para>
    135                             <para>To do so, Go to View, Reporters, click on
    136                                 <guibutton>Import</guibutton>. This starts a <guilabel>Reporter
    137                                     Importer Plugin</guilabel></para>
    138                             <para>More information about importing Reporters can be found in <xref
    139                                 linkend="reporters"/>
    140                             </para>
    141                         </listitem>
    142                     </orderedlist>
    143                 </listitem>
    144                
    145                 <listitem>
    146                     <para> Q: I am confused. What is the difference between <guilabel>Reporter map importer</guilabel>, <guilabel>Print map importer</guilabel>' and
    147                         <guilabel>Reporter importer</guilabel>?</para>
    148                     <para> A: Simple, A Reporter map importer plugin is used toload the Features associated to an ArrayDesign.
    149                         It allows you to understand where a Reporter has been spotted on a microarray glass slide </para>
    150                    
    151                     <para>A Reporter importer plugin should be used to load Reporter information into BASE2 </para>
    152                     <para>A Print Map importer plugin allows to understand which PCR plates where used and from which plate a Reporter came from.
    153                     The print map importer supports two formats: Biorobotics TAM format and Molecularware MWBR format. Theese are mapping files that connects plates with features and contains more or less only a bunch of coordinates. http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php
    154                         has a good description of both file formats.  So if you are only using commercial platforms or if you don't use plates in the array lims, you have no need for the print map importer.</para>
    155                 </listitem>
    156                
    157             </itemizedlist>
    158         </sect2>
    159        
    160  
    161 
    162 
    163         <sect2 id="faqs.global.biomaterial">
    164             <title>Biomaterial,Protocol, Hardware, Software related FAQS</title>
    165             <note>
    166                 <para> Note for BASE developers: BioSource pages implement a generic template that
    167                     seems to indicate that Protocols and inherited annotations can be associated to
    168                     BioSource Element. This should be modified. see distinction between primary and
    169                     inherited annotations, and the protocol parameter tag from the annotation tab
    170                     interface. </para>
    171             </note>
    172 
    173             <note>
    174                 <para> It is not possible to sort of the field from the Item view. </para>
    175             </note>
    176 
    177             <itemizedlist>
    178 
    179                 <listitem>
    180                     <para> Q: I have just created a new Item (A Sample in my case) but I can not see
    181                         it. Am I doing something wrong ? </para>
    182                     <para> A: Try clearing the filter. To do so: use the <guilabel>view /
    183                         presets</guilabel> dropdown and select the <guilabel>clear filter</guilabel>
    184                         entry. This will remove all characters in the search boxes and all
    185                         preselection of item in the drop down lists. If this does not solve your
    186                         problem, then check if the filter displays the item <guilabel>owned by
    187                         me</guilabel>. </para>
    188                 </listitem>
    189 
    190                 <listitem>
    191                     <para> Q: I can only see 3 columns from the Biosource List View but I know I
    192                         have a lot more information. Is there a way I can customize the column display? </para>
    193                     <para> A: Yes, you can display many more columns. To do so, do the following:</para>
    194                     <para>Click on the <guibutton>Column</guibutton> in the button bar. This will
    195                         display a window allowing you to select which fields to display and in
    196                         which order. For more information about this feature, please refer to the following section of the help note:
    197                             <xref linkend="webclient.figures.configure_columns"/> Note that in
    198                         BASE2, The same mechanism applies to all items. </para>
    199                 </listitem>
    200 
    201                 <listitem>
    202                     <para> Q: Is it possible to sort the values in a column from the Item List
    203                         View? </para>
    204                     <para> A: Of course it is. You can even sort on multiple columns. Please refer to the
    205                         help section for more information. <xref linkend="webclient.itemlist.filter"
    206                         />
    207                     </para>
    208                 </listitem>
    209 
    210                 <listitem>
    211                     <para> Q: Is it possible to sort the Annotation Types from Annotation tab in the
    212                         Biosource Item view </para>
    213                     <para> A: No. This is not possible at the moment. The page is static. </para>
    214                 </listitem>
    215 
    216                 <listitem>
    217                     <para> Q: I have to create pools of samples in my experiment due to scarcity of the biological material. Can I represent those pooled samples is
    218                         BASE2? </para>
    219                     <para> A: Yes, you can. This is a new features in BASE2 over BASE1. BASE2
    220                         graphical user interface features <guibutton>Pool...</guibutton> button and
    221                         Samples can be created from other samples. Please refer to the following
    222                         section of the help note: <xref linkend="sample.manage.createsample.pool"/>
    223                         Note that in BASE2, Pooling events can be represented for Samples, Extracts
    224                         and Labeled Extracts. </para>
    225                 </listitem>
    226 
    227                 <listitem>
    228                     <para> Q: I would like to add a Software Type in BASE2 but there is no button
    229                         for doing so. Is it possible ? </para>
    230                     <para> A: No, this is not possible. in BASE2, there is only one type of software at the moment.
    231                     </para>
    232                 </listitem>
    233 
    234                 <listitem>
    235                     <para> Q: I need to create a new Hardware type but the
    236                         <guibutton>New...</guibutton>button is grey and does not work. Why? </para>
    237 
    238                     <para>A: Your priviledges are not high enough and you have not been granted
    239                         permission to create Hardware Type. Contact your BASE2 administrator for
    240                         reviewing your priviledges.</para>
    241                     <para>To check your current priviledges, do the following</para>
    242                     <para> Go to <menuchoice>
    243                             <guimenu>Administrate</guimenu>
    244                             <guimenuitem>User</guimenuitem>
    245                         </menuchoice> use the search box under <guilabel>name</guilabel> or
    246                             <guilabel>login</guilabel> or <guilabel>email</guilabel> with relevant
    247                         information to get to your login details.</para>
    248                     <para> In the roles, columns, click on the hyperlinked value.</para>
    249                     <para> For more information about permissions, please refer to the dedicated
    250                         help page<xref linkend="user_administration"/>
    251                     </para>
    252                 </listitem>
    253 
    254 
    255                 <listitem>
    256                     <para> Q: I have created an Annotation Type 'Temperature' and shared it to
    257                         everyone but when I want to use it for annotating a Sample, I can not find
    258                         it ! How is that ? </para>
    259                     <para> A: The most likely explanation for this is that this particular
    260                         Annotation Type has been declared as Parameter. This means that it will only
    261                         be displayed in BASE2 when calling a protocols. Conversely, Should you have
    262                         declared an Annotation Type as regular one , it would not be made available
    263                         from the list of Possible Paramaters when declaring a Protocol. </para>
    264                 </listitem>
    265 
    266                 <listitem>
    267                     <para> Q: I have created an Annotation Type to annotate my samples, but I still
    268                         need to create another 40. Is there a way to speed up the manual entry ? </para>
    269                     <para> A: Yes. There is a CV loader plugin meant to just perform this tasks and
    270                         batch load your annotation types. You will have to create a tab delimited
    271                         files following a specified format detailed in help section <xref
    272                             linkend="annotations.manage.batchupload"/>. Once done, simply import the
    273                         file using the right plugin. </para>
    274                 </listitem>
    275 
    276                 <listitem>
    277                     <para> Q: When importing my Annotation Types from file, I made a mistake and all
    278                         are declared as parameters. How can I fix this? </para>
    279                     <para> A: Easy. Just modify your input file changing the parameter to no
    280                         wherever needed and run an import in update mode. This will change the
    281                         values stored in BASE2 to the one you want. </para>
    282                 </listitem>
    283 
    284                 <listitem>
    285                     <para>Q: I have read that I could batch-import an Experiment but I can not see
    286                         the <guibutton>import</guibutton> button from the interface. Why?</para>
    287 
    288                     <para>A: There are possible 2 explanations:</para>
    289                     <orderedlist>
    290                         <listitem>
    291                             <para>The import plugin is not installed on your BASE system. You
    292                                 therefore need to contact your BASE2 administrator or if you have
    293                                 the proper permissions you will have to install a plugin. More
    294                                 information about the plugin installation can be found in <xref
    295                                     linkend="plugins.installation"/>
    296                             </para>
    297                         </listitem>
    298                         <listitem>
    299                             <para>The import plugin is installed but you have no permissions for
    300                                 using it. Contact your system administrator and refer to the
    301                                 dedicated help page <xref linkend="user_administration"/>
    302                             </para>
    303                         </listitem>
    304                     </orderedlist>
    305                 </listitem>
    306 
    307                 <listitem>
    308                     <para> Q: I have carried out an experiment using both Affymetrix and Agilent
    309                         arrays but I can not select more than one raw data type in BASE2. What
    310                         should I do ? </para>
    311                     <para> A: In this particular case and because you are using 2 different raw data
    312                         file formats, you will have to split your experiment in 2. One experiment
    313                         for those samples processed using Affymetrix platform and another one using
    314                         Agilent platform. You don't necessarily have to provide all information
    315                         about the samples again but simply create new raw bioassay data which can be
    316                         grouped in a new experiment. </para>
    317                     <para> This is an important issue to bear in mind when creating Experiments in
    318                         BASE2</para>
    319                 </listitem>
    320 
    321             </itemizedlist>
    322         </sect2>
    323 
    324         <sect2 id="faqs.global.datafiles_rawdata">
    325             <title>Data Files and Raw Data related FAQs</title>
    326             <orderedlist>
    327 
    328                 <listitem>
    329                     <para> Q: What are the file formats supported by BASE2 ? </para>
    330                     <para> A: Please, refer to sections <xref
    331                         linkend="experiments_analysis.rawdatatypes"/> and <xref
    332                             linkend="appendix.rawdatatypes"/>for the full list of
    333                         supported file formats </para>
    334                 </listitem>
    335 
    336                 <listitem>
    337                     <para> Q: It seems that BASE2 does not support the datafiles generated by my
    338                         brand new scanner. Is it possible to add it to BASE2 ? </para>
    339                     <para> A: Yes it is possible to extend BASE2 so that it can support your system.</para>
    340                     <para>You will need first to define a new raw data type for BASE2 by modifying
    341                         the raw-datatypes.xml configuration file. </para>
    342                     <para>Then, you will have to perform an upgrade of the system. See section <xref
    343                             linkend="installation_upgrade"/></para>
    344                     <para>Finally, you will have to configure a raw data import plugin in order to
    345                         be able to create rawbioassays, refer to sections <xref
    346                             linkend="plugins.configuration"/> and <xref
    347                             linkend="experiments_analysis"/> for further information. </para>
    348                 </listitem>
    349 
    350                 <listitem>
    351                     <para> Q: I have created a raw bioassay which is not Affy but the system does
    352                         not allow me to upload a datafile whereas it is possible to do so if I
    353                         declared my rawbioassay of type Affy. Why? </para>
    354                     <para>A: This is normal. BASE2 deals with Affymetrix datafiles differently.
    355                         BASE2 stores native Affymetrix file and does not load the value in tables as
    356                         it does for other platforms.</para>
    357                     <para> For non-affymetrix rawbioassay, you will have to import the raw data
    358                         files and to do this you will need 3 things:</para>
    359                     <orderedlist>
    360                         <listitem>
    361                             <para> - have imported reporters attached to the array design, please
    362                                 refer to the relevant help section here <xref linkend="reporters"/>
    363                                 and <xref linkend="array_lims"/>
    364                             </para>
    365                         </listitem>
    366                         <listitem>
    367                             <para> - to make sure that your BASE2 instance is configured to support
    368                                 the file format. please refer to BASE2 configuration help page
    369                             </para>
    370                         </listitem>
    371                         <listitem>
    372                             <para> - need a rawdata import plugin properly configured, refer to
    373                                 section for more <xref linkend="plugins.configuration"/>
    374                                 <note>
    375                                     <para>Note also that it is possible to import plugin
    376                                         configuration as xml file. Please check the BASE2 page
    377                                         maintaining a <ulink
    378                                             url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"
    379                                             >list of plugin configurations</ulink>
    380                                     </para>
    381                                 </note>
    382                             </para>
    383                         </listitem>
    384                     </orderedlist>
    385                 </listitem>
    386                 <listitem>
    387                     <para> Q: I have created a raw bioassay using Affymetrix CEL file but the
    388                         interface says 'no spot'. I have really loaded the file ! Why ? </para>
    389                     <para> A: Again, this is because of the specific treatement of Affymetrix files
    390                         compared to other platforms. Please refer to FAQ 3 and help page <xref
    391                             linkend="experiments_analysis.rawbioassay.rawdata"/>
    392                     </para>
    393                 </listitem>
    394 
    395                 <listitem>
    396                     <para> Q: Are Affymetrix CTT and CAB files supported by BASE2 ? </para>
    397                     <para> A: There is no support for ddt or cab. Currently only cdf and cel files
    398                         are supported by the Affymetrix plug-ins. Annotation files (.csv) are used
    399                         for uploading probeset (reporter in BASE language) information. The issue of
    400                         supporting ddt and cab files is an import and a plug-in issue. There are two
    401                         ways to solve this: i) Write code that treats the file in a proper way and
    402                         submit the solution to the developer team (preferred route ;-) ). ii) Submit
    403                         a ticket through <ulink url="http://base.thep.lu.se"
    404                         >http://base.thep.lu.se</ulink> explaining what you'd like to see wrt to ddt
    405                         and cabs. Note, to include ddt and cab support to BASE, the file formats
    406                         must be open, that is we must be able to read them without proprietary
    407                         non-distributable code. </para>
    408                 </listitem>
    409 
    410 
    411                 <listitem>
    412                     <para> Q: Are Illumina datafiles supported by BASE2 ? </para>
    413                     <para> A: Yes, thanks to BASE2 user communities, you can find the following
    414                         information </para>
    415                     <para> Illumina conversion.txt (1.8 kB) - an R script to convert a multi-array
    416                         Illumina .csv output file into multiple single-array files.</para>
    417                     <para> raw-data-types.xml (92.0 kB) - Raw data types files edited by Jeremy
    418                         Davis-Turak (UCLA Department of Neurology) to include Illumina arrays</para>
    419                     <para>extended-properties.xml (5.2 kB) - Extended properties file edited by
    420                         Jeremy Davis-Turak (UCLA Department of Neurology) to include reporter
    421                         columns used by Illumina</para>
    422                     <para>see <ulink url="http://base.thep.lu.se/ticket/486">ticket 486</ulink> for
    423                         more information and download the files</para>
    424                 </listitem>
    425 
    426                 <listitem>
    427                     <para> Q: What About Agilent Files, the interface says they are not supported ? </para>
    428                     <para> A: Yes, thanks to BASE2 user communities, you can find the following
    429                         information </para>
    430                 </listitem>
    431 
    432 
    433                 <listitem>
    434                     <para> Q: What About Agilent Files, the interface says they are not supported ? </para>
    435                     <para> A: Yes, thanks to BASE2 user communities, you can find the following
    436                         information </para>
    437                 </listitem>
    438 
    439             </orderedlist>
    440         </sect2>
    441 
    442         <sect2 id="faqs.global.data_repositories">
    443             <title>Data Deposition to Public Repositories related FAQs</title>
    444 
    445             <itemizedlist>
    446                 <listitem>
    447                     <para> Q: I am asked by reviewers to deposit my microarray data in a public
    448                         repository. How can BASE2 help me ? </para>
    449                     <para> A: BASE2 has an export plugin which produces a tab2mage file accepted by
    450                         ArrayExpress. </para>
    451                     <para> However, for the plugin to work properly, a series of rules need to be
    452                         followed, please refer to section <xref linkend="annotations"/> for
    453                         additionnal information. </para>
    454                     <para> Once tab2mage file successfully exported, you will have to create an
    455                         archive containing all raw datafiles related to the experiment you want to
    456                         sent to ArrayExpress, with tab2mage file. More information about tab2mage
    457                         format can be found <ulink url="tab2mage.sourceforge.net">here</ulink></para>
    458                     <para> to send the submission to array express, use the following details:
    459                             <ulink url="ftp.ebi.ac.uk pwd">ArrayExpress FTP site</ulink>, using
    460                         login and password 'aexpress'. </para>
    461                     <warning>
    462                         <para> The current export plugin does not support tab2mage normalized and
    463                             transformed files, so some additional work might be required to be fully
    464                             complient, please refer to tab2mage helpnotes for creating these final
    465                             gene expression files and update the tab2mage files </para>
    466                     </warning>
    467 
    468                 </listitem>
    469 
    470                 <listitem>
    471                     <para>Q: Repositories want me to be MIAME compliant but How do i know that ?</para>
    472                     <para>A: BASE2 can help you in many ways to achieve MIAME compliance and
    473                         therefore facilitate your submissions</para>
    474                     <para>First, make sure to format your Annotation Types following the rules
    475                         detailed in <xref linkend="annotations.bestpractices"/></para>
    476                     <para>Then, before exporting, it is probably a good idee to run the
    477                             <guilabel>Experiment Overview</guilabel> detailed in <xref
    478                             linkend="experiments_analysis.experiment.overview"/>. By selecting
    479                         stringent criteria from the interface, the tool will detect all missing
    480                         information that could be requested by Repositories</para>
    481                     <para>Finally, if the Experiment Overview does not report any error any more,
    482                         you can run the tab2mage export plugin suitable for ArrayExpress at
    483                     EBI</para>
    484                 </listitem>
    485                
    486                 <listitem>
    487                     <para>
    488                         Q: I have exported in Tab2mage file, does it mean I am MIAME compliant ?
    489                     </para>
    490                     <para>
    491                         A: NO, not necessarily! Tab2mage exporter complies with Tab2mage specifications so you will be Tab2mage compliant.
    492                         However, MIAME compliance depends very much on the kind of annotation you have supplied. Please refer to the previous question for more information about how to check for MIAME compliance in BASE2 using the Experiment overview function.
    493                     </para>
    494                 </listitem>
    495                
    496                
    497 
    498                 <listitem>
    499                     <para> Q: I have deleted the datafiles from BASE2 file systems since I have
    500                         imported them in tables. So I don't have datafiles to send to ArrayExpress
    501                         anymore. </para>
    502                     <para> A: This is not a good news. In the absence of a data exporter, it is
    503                         advised to keep the native datafiles generated by scanners on the file
    504                         system and to name RawBioassays with the datafile names associated with it.
    505                         This ensures an easy tab2mage export. </para>
    506                 </listitem>
    507 
    508                 <listitem>
    509                     <para> Q: I have created pooled samples in BASE2. Can I export in tab2mage
    510                         format ? </para>
    511                     <para> A: No, sorry, not for the moment. In its current implementation, BASE2
    512                         tab2mage exporter does not support Pooling events. We are working on adding
    513                         this features in future version of the plugin. So watch the BASE2 plugin
    514                         space for upgrades. </para>
    515                 </listitem>
    516 
    517             </itemizedlist>
    518         </sect2>
    519 
    520  
    521 
    522         <sect2 id="faqs.global.analysis">
    523             <title>Analysis related FAQs</title>
    524             <itemizedlist>
    525 
    526                 <listitem>
    527                     <para> Q:Is it possible to use the FormulaFilter to filter for null fields (or
    528                         non null fields)? </para>
    529                     <para> A: </para>
    530                 </listitem>
    531 
    532                 <listitem>
    533                     <para> Q:OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
    534                         perform normalization on Affymetrix raw data ? </para>
    535                     <para> A: Yes, there is. BASE2 team has created a plugin based on
    536                         <ulink url="http://rmaexpress.bmbolstad.com/">here</ulink>
    537                                               RMAExpress methods
    538                         from Bolstad and Irizarry so you can normalize Affymetrix datasets of reasonable
    539                         size (not 1000 CEL files at a time though even though this might depend on your set-up...) </para>
    540                     <para>Additionnally, thanks to BASE2 web services, you can access BASE2 remotely
    541                         from R environment running on more powerfull machine for example. This can
    542                         give you more flexibility for performing normalization on large Affymetrix
    543                         data sets. </para>
    544                     <note>
    545                         <para>The web service currently only works for Affymetrix raw bioassays
    546                         </para>
    547                     </note>
    548                 </listitem>
    549 
    550             </itemizedlist>
    551         </sect2>
    552 
    553     </sect1>
    554 </chapter>
     5<!--
     6  $Id: faqs.xml 3246 2007-04-16 14:12:23Z martin $
     7 
     8  Copyright (C) Authors contributing to this file.
     9 
     10  This file is part of BASE - BioArray Software Environment.
     11  Available at http://base.thep.lu.se/
     12 
     13  BASE is free software; you can redistribute it and/or
     14  modify it under the terms of the GNU General Public License
     15  as published by the Free Software Foundation; either version 2
     16  of the License, or (at your option) any later version.
     17 
     18  BASE is distributed in the hope that it will be useful,
     19  but WITHOUT ANY WARRANTY; without even the implied warranty of
     20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     21  GNU General Public License for more details.
     22 
     23  You should have received a copy of the GNU General Public License
     24  along with this program; if not, write to the Free Software
     25  Foundation, Inc., 59 Temple Place - Suite 330,
     26  Boston, MA  02111-1307, USA.
     27-->
     28
     29<part id="faqs">
     30  <?dbhtml dir="faqs"?>
     31  <title>FAQs</title>
     32  <chapter id="faqs.global">
     33    <title>Frequently Asked Questions</title>
     34    <para />
     35    <sect1 id="faqs.global.reporter">
     36      <title>Reporters related FAQs</title>
     37      <qandaset defaultlabel='qanda'>
     38        <qandaentry>
     39          <question>
     40            <simpara>
     41              I can't find my favourite database for annotating Reporters. Can I add
     42              my database to BASE2 and if so, How should it proceed?
     43            </simpara>
     44          </question>
     45          <answer>
     46            <simpara>
     47              Yes, you can add resources to annotate Reporters. You will need to
     48              upgrade BASE2 and you may have to contact your system administrator for
     49              doing so.
     50            </simpara>
     51
     52            <simpara>
     53              In order to change, remove or add annotations fields attached to
     54              Reporters, you will need modify the extended-properties.xml file and run
     55              a BASE update. Please refer to section
     56              <xref linkend="installation_upgrade.installation" />
     57              for information about both processes. Once done with the upgrade, you'll
     58              have to defined a new reporter import plugin. Instructions can be found
     59              under
     60              <xref linkend="plugins" />
     61            </simpara>
     62          </answer>
     63        </qandaentry>
     64
     65        <qandaentry>
     66          <question>
     67            <simpara>
     68              I have made a mistake while loading my reporters. How can I delete them
     69              all in one go ?
     70            </simpara>
     71          </question>
     72          <answer>
     73            <simpara>
     74              Please contact your system administrator (maybe in the future use the
     75              reporter import plugin in delete mode)
     76            </simpara>
     77            <note>
     78              <simpara>
     79                Common problem: from the gui, one can only delete elements displayed
     80                from one given pages so how does one do in order to delete several
     81                thousands of reporters spread across several pages ?
     82              </simpara>
     83            </note>
     84          </answer>
     85        </qandaentry>
     86      </qandaset>
     87    </sect1>
     88
     89    <sect1 id="faqs.global.arraydesign">
     90      <title>ArrayDesign related FAQs</title>
     91      <qandaset defaultlabel='qanda'>
     92        <qandaentry>
     93          <question>
     94            <para>
     95              I have 20 Affymetrix ArrayDesigns to create from CDF files, is there a
     96              way to speed-up the creation process ?
     97            </para>
     98          </question>
     99          <answer>
     100            <para>
     101              Yes, you can use the Affymetrix CDF ArrayDesign plugin to do so. The
     102              plugin takes as argument as zipped archive containing CDF or CLF or
     103              BPMAP files. and then creates all ArrayDesign objects in BASE using the
     104              CDF files basename as Object Name.
     105              <note>
     106                <para>
     107                  The plugin should be used by Power User or Administrators only.
     108                </para>
     109              </note>
     110            </para>
     111          </answer>
     112        </qandaentry>
     113
     114        <qandaentry>
     115          <question>
     116            <para>What about gal files, is there something similar?</para>
     117          </question>
     118          <answer>
     119            <para>
     120              No, not quite yet as things are a bit more complicated. People are
     121              working on a plugin for help data entry.
     122            </para>
     123          </answer>
     124        </qandaentry>
     125
     126        <qandaentry>
     127          <question>
     128            <para>
     129              So What it the best way to create an ArrayDesign in BASE2 when starting
     130              from a gal file ?
     131            </para>
     132          </question>
     133          <answer>
     134            <para>
     135              Ok, this is a bit more work that with Affymetrix but here is the
     136              procedure to remember:
     137            </para>
     138            <para>
     139              A gal file tells where
     140              <guilabel>Reporters</guilabel>
     141              have been spotted on a Array. So a gal file can be used to do 2 things
     142            </para>
     143            <orderedlist>
     144              <listitem>
     145                <para>
     146                  -Define the features of an Array Design for a non-Affy platform
     147                  using a
     148                  <guilabel>Reporter Map importer plugin</guilabel>
     149                  .
     150                </para>
     151                <para>
     152                  To do so, after having created an New Array Design, go to the
     153                  Array Design Item view by clicking on the name of the newly
     154                  created Array Design
     155                </para>
     156                <para>
     157                  Click on the
     158                  <guibutton>Import</guibutton>
     159                  in the button. If you don't see it, it means that you have not
     160                  enough priviledges (contact the administrator)
     161                </para>
     162                <para>
     163                  This starts a plugin whose setting should be 'Reporter map
     164                  importer' and ' the file format should be 'gal file' (note this
     165                  has to been defined, if not present, please create the proper
     166                  reporter map plugin configuration.
     167                </para>
     168                <para>
     169                  Now, select File and fill in necessary information from the
     170                  wizard and run the plugin.
     171                </para>
     172                <para>
     173                  Once done (and if everything went fine), you can see from the
     174                  Array Design list view that on the Array Design list view page,
     175                  the
     176                  <guilabel>Has features</guilabel>
     177                  entry has been modified and is set to 'Yes (n)' where n
     178                  indicates the number of spots (features) for this array
     179                </para>
     180                <note>
     181                  <para>
     182                    Features can also be loaded from a Genepix gpr file
     183                    according to a very similar procedure but you will have to
     184                    create a specific reporter map importer plugin configuration
     185                    for such file before being able to proceed
     186                  </para>
     187                </note>
     188              </listitem>
     189              <listitem>
     190                <para>
     191                  -Define the
     192                  <guilabel>Reporters</guilabel>
     193                  present on this Array Design using
     194                  <guilabel>Reporter importer plugin</guilabel>
     195                  .
     196                </para>
     197                <para>
     198                  To do so, Go to View, Reporters, click on
     199                  <guibutton>Import</guibutton>
     200                  . This starts a
     201                  <guilabel>Reporter Importer Plugin</guilabel>
     202                </para>
     203                <para>
     204                  More information about importing Reporters can be found in
     205                  <xref linkend="reporters" />
     206                </para>
     207              </listitem>
     208            </orderedlist>
     209          </answer>
     210        </qandaentry>
     211
     212        <qandaentry>
     213          <question>
     214            <para>
     215              I am confused. What is the difference between
     216              <guilabel>Reporter map importer</guilabel>
     217              ,
     218              <guilabel>Print map importer</guilabel>
     219              ' and
     220              <guilabel>Reporter importer</guilabel>
     221              ?
     222            </para>
     223          </question>
     224          <answer>
     225            <para>
     226              Simple, A Reporter map importer plugin is used toload the Features
     227              associated to an ArrayDesign. It allows you to understand where a
     228              Reporter has been spotted on a microarray glass slide
     229            </para>
     230
     231            <para>
     232              A Reporter importer plugin should be used to load Reporter information
     233              into BASE2
     234            </para>
     235            <para>
     236              A Print Map importer plugin allows to understand which PCR plates where
     237              used and from which plate a Reporter came from. The print map importer
     238              supports two formats: Biorobotics TAM format and Molecularware MWBR
     239              format. Theese are mapping files that connects plates with features and
     240              contains more or less only a bunch of coordinates.
     241              http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php has
     242              a good description of both file formats. So if you are only using
     243              commercial platforms or if you don't use plates in the array lims, you
     244              have no need for the print map importer.
     245            </para>
     246          </answer>
     247        </qandaentry>
     248      </qandaset>
     249    </sect1>
     250
     251    <sect1 id="faqs.global.biomaterial">
     252      <title>Biomaterial,Protocol, Hardware, Software related FAQS</title>
     253      <qandaset defaultlabel='qanda'>
     254        <note>
     255          <para>
     256            Note for BASE developers: BioSource pages implement a generic template that
     257            seems to indicate that Protocols and inherited annotations can be associated
     258            to BioSource Element. This should be modified. see distinction between
     259            primary and inherited annotations, and the protocol parameter tag from the
     260            annotation tab interface.
     261          </para>
     262        </note>
     263
     264        <note>
     265          <para>It is not possible to sort of the field from the Item view.</para>
     266        </note>
     267        <qandaentry>
     268          <question>
     269            <para>
     270              I have just created a new Item (A Sample in my case) but I can not see
     271              it. Am I doing something wrong ?
     272            </para>
     273          </question>
     274          <answer>
     275            <para>
     276              Try clearing the filter. To do so: use the
     277              <guilabel>view / presets</guilabel>
     278              dropdown and select the
     279              <guilabel>clear filter</guilabel>
     280              entry. This will remove all characters in the search boxes and all
     281              preselection of item in the drop down lists. If this does not solve your
     282              problem, then check if the filter displays the item
     283              <guilabel>owned by me</guilabel>
     284              .
     285            </para>
     286          </answer>
     287        </qandaentry>
     288
     289        <qandaentry>
     290          <question>
     291            <para>
     292              I can only see 3 columns from the Biosource List View but I know I have
     293              a lot more information. Is there a way I can customize the column
     294              display?
     295            </para>
     296          </question>
     297          <answer>
     298            <para>
     299              Yes, you can display many more columns. To do so, do the following:
     300            </para>
     301            <para>
     302              Click on the
     303              <guibutton>Column</guibutton>
     304              in the button bar. This will display a window allowing you to select
     305              which fields to display and in which order. For more information about
     306              this feature, please refer to the following section of the help note:
     307              <xref linkend="webclient.figures.configure_columns" />
     308              Note that in BASE2, The same mechanism applies to all items.
     309            </para>
     310          </answer>
     311        </qandaentry>
     312
     313        <qandaentry>
     314          <question>
     315            <para>
     316              Is it possible to sort the values in a column from the Item List View?
     317            </para>
     318          </question>
     319          <answer>
     320            <para>
     321              Of course it is. You can even sort on multiple columns. Please refer to
     322              the help section for more information.
     323              <xref linkend="webclient.itemlist.filter" />
     324            </para>
     325          </answer>
     326        </qandaentry>
     327
     328        <qandaentry>
     329          <question>
     330            <para>
     331              Is it possible to sort the Annotation Types from Annotation tab in the
     332              Biosource Item view
     333            </para>
     334          </question>
     335          <answer>
     336            <para>No. This is not possible at the moment. The page is static.</para>
     337          </answer>
     338        </qandaentry>
     339
     340        <qandaentry>
     341          <question>
     342            <para>
     343              I have to create pools of samples in my experiment due to scarcity of
     344              the biological material. Can I represent those pooled samples is BASE2?
     345            </para>
     346          </question>
     347          <answer>
     348            <para>
     349              Yes, you can. This is a new features in BASE2 over BASE1. BASE2
     350              graphical user interface features
     351              <guibutton>Pool...</guibutton>
     352              button and Samples can be created from other samples. Please refer to
     353              the following section of the help note:
     354              <xref linkend="sample.manage.createsample.pool" />
     355              Note that in BASE2, Pooling events can be represented for Samples,
     356              Extracts and Labeled Extracts.
     357            </para>
     358          </answer>
     359        </qandaentry>
     360        <qandaentry>
     361          <question>
     362            <para>
     363              I would like to add a Software Type in BASE2 but there is no button for
     364              doing so. Is it possible ?
     365            </para>
     366          </question>
     367          <answer>
     368            <para>
     369              No, this is not possible. in BASE2, there is only one type of software
     370              at the moment.
     371            </para>
     372          </answer>
     373        </qandaentry>
     374
     375        <qandaentry>
     376          <question>
     377            <para>
     378              I need to create a new Hardware type but the
     379              <guibutton>New...</guibutton>
     380              button is grey and does not work. Why?
     381            </para>
     382          </question>
     383          <answer>
     384            <para>
     385              Your priviledges are not high enough and you have not been granted
     386              permission to create Hardware Type. Contact your BASE2 administrator for
     387              reviewing your priviledges.
     388            </para>
     389            <para>To check your current priviledges, do the following</para>
     390            <para>
     391              Go to
     392              <menuchoice>
     393                <guimenu>Administrate</guimenu>
     394                <guimenuitem>User</guimenuitem>
     395              </menuchoice>
     396              use the search box under
     397              <guilabel>name</guilabel>
     398              or
     399              <guilabel>login</guilabel>
     400              or
     401              <guilabel>email</guilabel>
     402              with relevant information to get to your login details.
     403            </para>
     404            <para>In the roles, columns, click on the hyperlinked value.</para>
     405            <para>
     406              For more information about permissions, please refer to the dedicated
     407              help page
     408              <xref linkend="user_administration" />
     409            </para>
     410          </answer>
     411        </qandaentry>
     412        <qandaentry>
     413          <question>
     414            <para>
     415              I have created an Annotation Type 'Temperature' and shared it to
     416              everyone but when I want to use it for annotating a Sample, I can not
     417              find it ! How is that ?
     418            </para>
     419          </question>
     420          <answer>
     421            <para>
     422              The most likely explanation for this is that this particular Annotation
     423              Type has been declared as Parameter. This means that it will only be
     424              displayed in BASE2 when calling a protocols. Conversely, Should you have
     425              declared an Annotation Type as regular one , it would not be made
     426              available from the list of Possible Paramaters when declaring a
     427              Protocol.
     428            </para>
     429          </answer>
     430        </qandaentry>
     431
     432        <qandaentry>
     433          <question>
     434            <para>
     435              I have created an Annotation Type to annotate my samples, but I still
     436              need to create another 40. Is there a way to speed up the manual entry ?
     437            </para>
     438          </question>
     439          <answer>
     440            <para>
     441              Yes. There is a CV loader plugin meant to just perform this tasks and
     442              batch load your annotation types. You will have to create a tab
     443              delimited files following a specified format detailed in help section
     444              <xref linkend="annotations.manage.batchupload" />
     445              . Once done, simply import the file using the right plugin.
     446            </para>
     447          </answer>
     448        </qandaentry>
     449
     450        <qandaentry>
     451          <question>
     452            <para>
     453              When importing my Annotation Types from file, I made a mistake and all
     454              are declared as parameters. How can I fix this?
     455            </para>
     456          </question>
     457          <answer>
     458            <para>
     459              Easy. Just modify your input file changing the parameter to no wherever
     460              needed and run an import in update mode. This will change the values
     461              stored in BASE2 to the one you want.
     462            </para>
     463          </answer>
     464        </qandaentry>
     465
     466        <qandaentry>
     467          <question>
     468            <para>
     469              I have read that I could batch-import an Experiment but I can not see
     470              the
     471              <guibutton>import</guibutton>
     472              button from the interface. Why?
     473            </para>
     474          </question>
     475          <answer>
     476            <para>There are possible 2 explanations:</para>
     477            <orderedlist>
     478              <listitem>
     479                <para>
     480                  The import plugin is not installed on your BASE system. You
     481                  therefore need to contact your BASE2 administrator or if you
     482                  have the proper permissions you will have to install a plugin.
     483                  More information about the plugin installation can be found in
     484                  <xref linkend="plugins.installation" />
     485                </para>
     486              </listitem>
     487              <listitem>
     488                <para>
     489                  The import plugin is installed but you have no permissions for
     490                  using it. Contact your system administrator and refer to the
     491                  dedicated help page
     492                  <xref linkend="user_administration" />
     493                </para>
     494              </listitem>
     495            </orderedlist>
     496          </answer>
     497        </qandaentry>
     498
     499        <qandaentry>
     500          <question>
     501            <para>
     502              I have carried out an experiment using both Affymetrix and Agilent
     503              arrays but I can not select more than one raw data type in BASE2. What
     504              should I do ?
     505            </para>
     506          </question>
     507          <answer>
     508            <para>
     509              In this particular case and because you are using 2 different raw data
     510              file formats, you will have to split your experiment in 2. One
     511              experiment for those samples processed using Affymetrix platform and
     512              another one using Agilent platform. You don't necessarily have to
     513              provide all information about the samples again but simply create new
     514              raw bioassay data which can be grouped in a new experiment.
     515            </para>
     516            <para>
     517              This is an important issue to bear in mind when creating Experiments in
     518              BASE2
     519            </para>
     520          </answer>
     521        </qandaentry>
     522      </qandaset>
     523    </sect1>
     524
     525    <sect1 id="faqs.global.datafiles_rawdata">
     526      <title>Data Files and Raw Data related FAQs</title>
     527      <qandaset defaultlabel='qanda'>
     528        <qandaentry>
     529          <question>
     530            <para>What are the file formats supported by BASE2 ?</para>
     531          </question>
     532          <answer>
     533            <para>
     534              Please, refer to sections
     535              <xref linkend="experiments_analysis.rawdatatypes" />
     536              and
     537              <xref linkend="appendix.rawdatatypes" />
     538              for the full list of supported file formats
     539            </para>
     540          </answer>
     541        </qandaentry>
     542
     543        <qandaentry>
     544          <question>
     545            <para>
     546              It seems that BASE2 does not support the datafiles generated by my brand
     547              new scanner. Is it possible to add it to BASE2 ?
     548            </para>
     549          </question>
     550          <answer>
     551            <para>
     552              Yes it is possible to extend BASE2 so that it can support your system.
     553            </para>
     554            <para>
     555              You will need first to define a new raw data type for BASE2 by modifying
     556              the raw-datatypes.xml configuration file.
     557            </para>
     558            <para>
     559              Then, you will have to perform an upgrade of the system. See section
     560              <xref linkend="installation_upgrade" />
     561            </para>
     562            <para>
     563              Finally, you will have to configure a raw data import plugin in order to
     564              be able to create rawbioassays, refer to sections
     565              <xref linkend="plugins.configuration" />
     566              and
     567              <xref linkend="experiments_analysis" />
     568              for further information.
     569            </para>
     570          </answer>
     571        </qandaentry>
     572
     573        <qandaentry>
     574          <question>
     575            <para>
     576              I have created a raw bioassay which is not Affy but the system does not
     577              allow me to upload a datafile whereas it is possible to do so if I
     578              declared my rawbioassay of type Affy. Why?
     579            </para>
     580          </question>
     581          <answer>
     582            <para>
     583              This is normal. BASE2 deals with Affymetrix datafiles differently. BASE2
     584              stores native Affymetrix file and does not load the value in tables as
     585              it does for other platforms.
     586            </para>
     587            <para>
     588              For non-affymetrix rawbioassay, you will have to import the raw data
     589              files and to do this you will need 3 things:
     590            </para>
     591            <orderedlist>
     592              <listitem>
     593                <para>
     594                  - have imported reporters attached to the array design, please
     595                  refer to the relevant help section here
     596                  <xref linkend="reporters" />
     597                  and
     598                  <xref linkend="array_lims" />
     599                </para>
     600              </listitem>
     601              <listitem>
     602                <para>
     603                  - to make sure that your BASE2 instance is configured to support
     604                  the file format. please refer to BASE2 configuration help page
     605                </para>
     606              </listitem>
     607              <listitem>
     608                <para>
     609                  - need a rawdata import plugin properly configured, refer to
     610                  section for more
     611                  <xref linkend="plugins.configuration" />
     612                  <note>
     613                    <para>
     614                      Note also that it is possible to import plugin
     615                      configuration as xml file. Please check the BASE2 page
     616                      maintaining a
     617                      <ulink
     618                        url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html">
     619                        list of plugin configurations
     620                      </ulink>
     621                    </para>
     622                  </note>
     623                </para>
     624              </listitem>
     625            </orderedlist>
     626          </answer>
     627        </qandaentry>
     628
     629        <qandaentry>
     630          <question>
     631            <para>
     632              I have created a raw bioassay using Affymetrix CEL file but the
     633              interface says 'no spot'. I have really loaded the file ! Why ?
     634            </para>
     635          </question>
     636          <answer>
     637            <para>
     638              Again, this is because of the specific treatement of Affymetrix files
     639              compared to other platforms. Please refer to FAQ 3 and help page
     640              <xref linkend="experiments_analysis.rawbioassay.rawdata" />
     641            </para>
     642          </answer>
     643        </qandaentry>
     644
     645        <qandaentry>
     646          <question>
     647            <para>Are Affymetrix CTT and CAB files supported by BASE2 ?</para>
     648          </question>
     649          <answer>
     650            <para>
     651              There is no support for ddt or cab. Currently only cdf and cel files are
     652              supported by the Affymetrix plug-ins. Annotation files (.csv) are used
     653              for uploading probeset (reporter in BASE language) information. The
     654              issue of supporting ddt and cab files is an import and a plug-in issue.
     655              There are two ways to solve this: i) Write code that treats the file in
     656              a proper way and submit the solution to the developer team (preferred
     657              route ;-) ). ii) Submit a ticket through
     658              <ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
     659              explaining what you'd like to see wrt to ddt and cabs. Note, to include
     660              ddt and cab support to BASE, the file formats must be open, that is we
     661              must be able to read them without proprietary non-distributable code.
     662            </para>
     663          </answer>
     664        </qandaentry>
     665
     666        <qandaentry>
     667          <question>
     668            <para>Are Illumina datafiles supported by BASE2 ?</para>
     669          </question>
     670          <answer>
     671            <para>
     672              Yes, thanks to BASE2 user communities, you can find the following
     673              information
     674            </para>
     675            <para>
     676              Illumina conversion.txt (1.8 kB) - an R script to convert a multi-array
     677              Illumina .csv output file into multiple single-array files.
     678            </para>
     679            <para>
     680              raw-data-types.xml (92.0 kB) - Raw data types files edited by Jeremy
     681              Davis-Turak (UCLA Department of Neurology) to include Illumina arrays
     682            </para>
     683            <para>
     684              extended-properties.xml (5.2 kB) - Extended properties file edited by
     685              Jeremy Davis-Turak (UCLA Department of Neurology) to include reporter
     686              columns used by Illumina
     687            </para>
     688            <para>
     689              see
     690              <ulink url="http://base.thep.lu.se/ticket/486">ticket 486</ulink>
     691              for more information and download the files
     692            </para>
     693          </answer>
     694        </qandaentry>
     695
     696        <qandaentry>
     697          <question>
     698            <para>
     699              What About Agilent Files, the interface says they are not supported ?
     700            </para>
     701          </question>
     702          <answer>
     703            <para>
     704              Yes, thanks to BASE2 user communities, you can find the following
     705              information
     706            </para>
     707          </answer>
     708        </qandaentry>
     709
     710        <qandaentry>
     711          <question>
     712            <para>
     713              What About Agilent Files, the interface says they are not supported ?
     714            </para>
     715          </question>
     716          <answer>
     717            <para>
     718              Yes, thanks to BASE2 user communities, you can find the following
     719              information
     720            </para>
     721          </answer>
     722        </qandaentry>
     723      </qandaset>
     724    </sect1>
     725
     726    <sect1 id="faqs.global.data_repositories">
     727      <title>Data Deposition to Public Repositories related FAQs</title>
     728      <qandaset defaultlabel='qanda'>
     729        <qandaentry>
     730          <question>
     731            <para>
     732              I am asked by reviewers to deposit my microarray data in a public
     733              repository. How can BASE2 help me ?
     734            </para>
     735          </question>
     736          <answer>
     737            <para>
     738              BASE2 has an export plugin which produces a tab2mage file accepted by
     739              ArrayExpress.
     740            </para>
     741            <para>
     742              However, for the plugin to work properly, a series of rules need to be
     743              followed, please refer to section
     744              <xref linkend="annotations" />
     745              for additionnal information.
     746            </para>
     747            <para>
     748              Once tab2mage file successfully exported, you will have to create an
     749              archive containing all raw datafiles related to the experiment you want
     750              to sent to ArrayExpress, with tab2mage file. More information about
     751              tab2mage format can be found
     752              <ulink url="tab2mage.sourceforge.net">here</ulink>
     753            </para>
     754            <para>
     755              to send the submission to array express, use the following details:
     756              <ulink url="ftp.ebi.ac.uk pwd">ArrayExpress FTP site</ulink>
     757              , using login and password 'aexpress'.
     758            </para>
     759            <warning>
     760              <para>
     761                The current export plugin does not support tab2mage normalized and
     762                transformed files, so some additional work might be required to be
     763                fully complient, please refer to tab2mage helpnotes for creating
     764                these final gene expression files and update the tab2mage files
     765              </para>
     766            </warning>
     767          </answer>
     768        </qandaentry>
     769
     770        <qandaentry>
     771          <question>
     772            <para>
     773              Repositories want me to be MIAME compliant but How do i know that ?
     774            </para>
     775          </question>
     776          <answer>
     777            <para>
     778              BASE2 can help you in many ways to achieve MIAME compliance and
     779              therefore facilitate your submissions
     780            </para>
     781            <para>
     782              First, make sure to format your Annotation Types following the rules
     783              detailed in
     784              <xref linkend="annotations.bestpractices" />
     785            </para>
     786            <para>
     787              Then, before exporting, it is probably a good idee to run the
     788              <guilabel>Experiment Overview</guilabel>
     789              detailed in
     790              <xref linkend="experiments_analysis.experiment.overview" />
     791              . By selecting stringent criteria from the interface, the tool will
     792              detect all missing information that could be requested by Repositories
     793            </para>
     794            <para>
     795              Finally, if the Experiment Overview does not report any error any more,
     796              you can run the tab2mage export plugin suitable for ArrayExpress at EBI
     797            </para>
     798          </answer>
     799        </qandaentry>
     800
     801        <qandaentry>
     802          <question>
     803            <para>
     804              I have exported in Tab2mage file, does it mean I am MIAME compliant ?
     805            </para>
     806          </question>
     807          <answer>
     808            <para>
     809              NO, not necessarily! Tab2mage exporter complies with Tab2mage
     810              specifications so you will be Tab2mage compliant. However, MIAME
     811              compliance depends very much on the kind of annotation you have
     812              supplied. Please refer to the previous question for more information
     813              about how to check for MIAME compliance in BASE2 using the Experiment
     814              overview function.
     815            </para>
     816          </answer>
     817        </qandaentry>
     818
     819        <qandaentry>
     820          <question>
     821            <para>
     822              I have deleted the datafiles from BASE2 file systems since I have
     823              imported them in tables. So I don't have datafiles to send to
     824              ArrayExpress anymore.
     825            </para>
     826          </question>
     827          <answer>
     828            <para>
     829              This is not a good news. In the absence of a data exporter, it is
     830              advised to keep the native datafiles generated by scanners on the file
     831              system and to name RawBioassays with the datafile names associated with
     832              it. This ensures an easy tab2mage export.
     833            </para>
     834          </answer>
     835        </qandaentry>
     836
     837        <qandaentry>
     838          <question>
     839            <para>
     840              I have created pooled samples in BASE2. Can I export in tab2mage format
     841              ?
     842            </para>
     843          </question>
     844          <answer>
     845            <para>
     846              No, sorry, not for the moment. In its current implementation, BASE2
     847              tab2mage exporter does not support Pooling events. We are working on
     848              adding this features in future version of the plugin. So watch the BASE2
     849              plugin space for upgrades.
     850            </para>
     851          </answer>
     852        </qandaentry>
     853      </qandaset>
     854    </sect1>
     855
     856    <sect1 id="faqs.global.analysis">
     857      <title>Analysis related FAQs</title>
     858      <qandaset defaultlabel='qanda'>
     859        <qandaentry>
     860          <question>
     861            <para>
     862              Is it possible to use the FormulaFilter to filter for null fields (or
     863              non null fields)?
     864            </para>
     865          </question>
     866          <answer>
     867            <para></para>
     868          </answer>
     869        </qandaentry>
     870
     871        <qandaentry>
     872          <question>
     873            <para>
     874              OK, I have uploaded 40 CEL files in BASE2 but are there any tool to
     875              perform normalization on Affymetrix raw data ?
     876            </para>
     877          </question>
     878          <answer>
     879            <para>
     880              Yes, there is. BASE2 team has created a plugin based on
     881              <ulink url="http://rmaexpress.bmbolstad.com/">here</ulink>
     882              RMAExpress methods from Bolstad and Irizarry so you can normalize
     883              Affymetrix datasets of reasonable size (not 1000 CEL files at a time
     884              though even though this might depend on your set-up...)
     885            </para>
     886            <para>
     887              Additionnally, thanks to BASE2 web services, you can access BASE2
     888              remotely from R environment running on more powerfull machine for
     889              example. This can give you more flexibility for performing normalization
     890              on large Affymetrix data sets.
     891            </para>
     892            <note>
     893              <para>
     894                The web service currently only works for Affymetrix raw bioassays
     895              </para>
     896            </note>
     897          </answer>
     898        </qandaentry>
     899      </qandaset>
     900    </sect1>
     901  </chapter>
     902</part>

  • trunk/doc/src/docbook/index.xml

    r3334 r3386  
    3636  <include file="admindoc/index.xml"/>
    3737  <include file="developerdoc/index.xml"/>
     38  <include file="faq/faqs.xml" />
    3839  <include file="appendix/index.xml" />
    3940</book>

  • trunk/doc/src/docbook/userdoc/index.xml

    r3372 r3386  
    4444  <include file="experiments_analysis.xml"/>
    4545  <include file="import_export_data.xml"/>
    46   <include file="faqs.xml"/>
    4746</part>
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