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1	<?xml version="1.0" encoding="UTF-8"?>
2	<!DOCTYPE chapter PUBLIC
3	"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4	"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
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6	$Id: faqs.xml 3246 2007-04-16 14:12:23Z martin $
7
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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	<listiem>
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	</listiem>
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>

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