Changeset 3386
- Timestamp:
- May 25, 2007, 5:11:19 PM (16 years ago)
- Location:
- trunk
- Files:
-
- 1 added
- 3 edited
- 1 moved
Legend:
- Unmodified
- Added
- Removed
-
trunk/build.xml
r3382 r3386 1054 1054 <mkdir dir="${doc}/docbook/html/userdoc/trashcan"/> 1055 1055 <mkdir dir="${doc}/docbook/html/userdoc/webclient"/> 1056 <mkdir dir="${doc}/docbook/html/faqs" /> 1056 1057 1057 1058 <mkdir dir="${build}/docbook/html" /> -
trunk/doc/src/docbook/faq/faqs.xml
r3382 r3386 1 1 <?xml version="1.0" encoding="UTF-8"?> 2 <!DOCTYPE chapterPUBLIC2 <!DOCTYPE part PUBLIC 3 3 "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" 4 4 "../../../../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 36 36 <include file="admindoc/index.xml"/> 37 37 <include file="developerdoc/index.xml"/> 38 <include file="faq/faqs.xml" /> 38 39 <include file="appendix/index.xml" /> 39 40 </book> -
trunk/doc/src/docbook/userdoc/index.xml
r3372 r3386 44 44 <include file="experiments_analysis.xml"/> 45 45 <include file="import_export_data.xml"/> 46 <include file="faqs.xml"/>47 46 </part>
Note: See TracChangeset
for help on using the changeset viewer.