source: trunk/doc/src/docbook/userdoc/experiments.xml @ 3394

Last change on this file since 3394 was 3394, checked in by Martin Svensson, 14 years ago

Replaced the most common guibutton:s with entities

File size: 27.0 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE sect1 PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: experiments_analysis.xml 3308 2007-05-08 12:34:07Z nicklas $
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<sect1 id="experiments_analysis.experiments">
30  <title>Experiments</title>
31  <para>
32    Experiments are the starting point for analysis. When you have
33    uploaded and imported your raw data, collected and registered all
34    information and annotations about samples, hybridizations, and other
35    items, it is time to collect everything in an experiment.
36  </para>
37 
38  <para>
39    To create a new experiment you can either mark one ore more
40    raw biossays on the raw bioassays list view and use the
41    <guibutton>New experiment</guibutton> button. You can also
42    create a new experiment from the experiments list view.
43  </para>
44
45  <sect2 id="experiments_analysis.experiment.properties">
46    <title>Experiment properties</title>
47   
48    <figure id="experiments_analysis.figures.experiment_properties">
49      <title>Create experiment</title>
50      <screenshot>
51        <mediaobject>
52          <imageobject><imagedata 
53            fileref="figures/experiment_properties.png" format="PNG"
54            /></imageobject>
55        </mediaobject>
56      </screenshot>
57    </figure>         
58   
59   
60    <helptext external_id="experiment.edit" title="Edit experiment">
61   
62      <variablelist>
63      <varlistentry>
64        <term><guilabel>Name</guilabel></term>
65        <listitem>
66          <para>
67            The name of the experiment.
68          </para>
69        </listitem>
70      </varlistentry>
71     
72      <varlistentry>
73        <term><guilabel>Raw data type</guilabel></term>
74        <listitem>
75          <para>
76            The raw data type to use in the experiment. All raw bioassays
77            must have raw data with this type.
78          </para>
79        </listitem>
80      </varlistentry>
81
82      <varlistentry>
83        <term><guilabel>Directory</guilabel></term>
84        <listitem>
85          <para>
86            A directory in the BASE file system where plug-ins
87            can save files that are generated during the analysis.
88            This is optional and if not given the plug-ins must ask
89            about a directory each time they need it. Use the
90            <guibutton>Select</guibutton> button to browse the file system
91            or create a new directory.
92          </para>
93        </listitem>
94      </varlistentry>
95     
96      <varlistentry>
97        <term><guilabel>Raw bioassays</guilabel></term>
98        <listitem>
99          <para>
100            The raw bioassays you want to analyze in this experiment. If
101            you created the experiment from the raw bioassays list the
102            selected raw bioassays are already filled in. Use the
103            <guibutton>Add raw bioassays</guibutton> button to add more
104            raw bioassays or the &gbRemove; button
105            to remove the selected raw bioassays from the list.
106          </para>
107        </listitem>
108      </varlistentry>
109     
110      <varlistentry>
111        <term><guilabel>Description</guilabel></term>
112        <listitem>
113          <para>
114            A description of the experiment.
115          </para>
116        </listitem>
117      </varlistentry>
118
119      </variablelist>
120     
121      <para>
122        Click on the &gbSave; button to save the
123        changes or on &gbCancel; to abort.
124      </para>
125     
126      <seeother>
127        <other external_id="experiment.edit.publication">Publication</other>
128        <other external_id="experiment.edit.factors">Experimental factors</other>
129      </seeother>
130    </helptext>
131   
132    <sect3 id="experiments_analysis.experiment.publication">
133      <title>The publication tab</title>
134     
135      <helptext external_id="experiment.edit.publication" 
136        title="Experiment publication">
137
138        <para>
139          On this tab you can enter information about a publication
140          that is the result of the experiment. All of this information
141          is optional.
142        </para>
143       
144        <variablelist>
145        <varlistentry>
146          <term><guilabel>PubMedId</guilabel></term>
147          <listitem>
148            <para>
149              The ID of the publication in the
150              <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html"
151                >PubMed</ulink> database.
152            </para>
153          </listitem>
154        </varlistentry>
155        <varlistentry>
156          <term><guilabel>Title</guilabel></term>
157          <listitem>
158            <para>
159              The title of the publication.
160            </para>
161          </listitem>
162        </varlistentry>
163        <varlistentry>
164          <term><guilabel>Publication date</guilabel></term>
165          <listitem>
166            <para>
167              The date the article was published. Use the
168              <guibutton>Calendar</guibutton> button to select
169              a date from a popup window.
170            </para>
171          </listitem>
172        </varlistentry>
173        <varlistentry>
174          <term><guilabel>Abstract</guilabel></term>
175          <listitem>
176            <para>
177              The article abstract.
178            </para>
179          </listitem>
180        </varlistentry>
181        <varlistentry>
182          <term><guilabel>Experiment design</guilabel></term>
183          <listitem>
184            <para>
185              An explanation of the experiment design.
186            </para>
187          </listitem>
188        </varlistentry>
189        <varlistentry>
190          <term><guilabel>Experiment type</guilabel></term>
191          <listitem>
192            <para>
193              A description of the experiment type.
194            </para>
195          </listitem>
196        </varlistentry>
197        <varlistentry>
198          <term><guilabel>Affiliations</guilabel></term>
199          <listitem>
200            <para>
201              Partners and other related organisations that
202              have helped with the experiment.
203            </para>
204          </listitem>
205        </varlistentry>
206        <varlistentry>
207          <term><guilabel>Authors</guilabel></term>
208          <listitem>
209            <para>
210              The list of authors of the publication.
211            </para>
212          </listitem>
213        </varlistentry>
214        <varlistentry>
215          <term><guilabel>Publication</guilabel></term>
216          <listitem>
217            <para>
218              The body text of the publication.
219            </para>
220          </listitem>
221        </varlistentry>
222        </variablelist>
223       
224        <para>
225          Click on the &gbSave; button to save the
226          changes or on &gbCancel; to abort.
227        </para>
228     
229        <seeother>
230          <other external_id="experiment.edit">Experiment properties</other>
231          <other external_id="experiment.edit.factors">Experimental factors</other>
232        </seeother>
233      </helptext>
234    </sect3>
235   
236  </sect2>
237 
238  <sect2 id="experiments_analysis.experiment.factors">
239    <title>Experimental factors</title>
240   
241    <helptext external_id="experiment.edit.factors" 
242      title="Experimental factors">
243   
244      <para>
245        The experimental factors of an experiment are the variables
246        you are studying in the experiment. Typically the value of
247        an experimental factor is varied between samples or group of samples.
248        Different treatment methods is an example of an experimental factor.
249      </para>
250     
251      <para>
252        In the BASE world an experimental factor is the same as an annotation
253        type. Since you probably have lots of annotations on your items that are not
254        relevant for the experiment you must select the annotations types
255        that should make up the experimental factors of the experiment.
256      </para>
257     
258      <para>
259        Use the <guibutton>Add annotation types</guibutton> button to
260        select the annotation types that should be used as experimental
261        factors. The &gbRemove; button removes the
262        selected annotation types.
263      </para>
264
265      <para>
266        Click on the &gbSave; button to save the
267        changes or on &gbCancel; to abort.
268      </para>
269     
270      <para>
271        To be able to use the values of the experimental factors
272        in the analysis of your data the values must be accessible
273        from the raw bioassays. Since most of your annotations are
274        probably made at the sample level the raw bioassays must
275        inherit those annotations.
276        <nohelp>Read <xref linkend="annotations" /> 
277        for more information about this.</nohelp>
278      </para>
279     
280      <tip>
281        <para>
282        Use the <guilabel>Experiment overview</guilabel> function to
283        verify that all your raw bioassays has been annotated or
284        inherited values for all experimental factors. If not, you
285        should do that before starting with the analysis.
286        </para>
287      </tip>
288     
289      <seeother>
290        <other external_id="experiment.edit">Experiment properties</other>
291        <other external_id="experiment.edit.publication">Publication</other>
292        <other external_id="experiment.overview">Experiment overview</other>
293        <other external_id="annotations.edit.inerited">Inherit annotations</other>
294      </seeother>
295     
296    </helptext>
297  </sect2>
298
299 
300  <sect2 id="experiments_analysis.experiment.overview">
301    <title>Experiment overview</title>
302   
303    <para>
304      With the <guilabel>Experiment overview</guilabel> 
305      function you can get an overview of all hybridizations,
306      extracts, samples, annotations, etc. used in an
307      experiment. The overview includes a lot of checks
308      that validates your experimental setup for missing
309      or possibly incorrect information.
310    </para>
311   
312    <para>
313      You can access the overview of an experiment by navigating
314      to the single-item view of the experiment you are interested in.
315      Then, switch to the <guilabel>Overview</guilabel> tab that
316      is present on that page. Here is an example of what is displayed:
317    </para>
318   
319    <figure id="experiments_analysis.figures.experimentoverview">
320      <title>The experiment overview</title>
321      <screenshot>
322        <mediaobject>
323          <imageobject><imagedata 
324            fileref="figures/experiment_overview.png" format="PNG"
325            /></imageobject>
326        </mediaobject>
327      </screenshot>
328    </figure>
329   
330    <helptext external_id="experiment.overview" 
331      title="Experiment overview">
332    <para>
333      The page is divided into three sections:
334    </para>
335   
336    <itemizedlist>
337      <listitem>
338        <para>
339        To the left is a tree displaying all items
340        in the experiment and how they are linked to
341        each other.
342        </para>
343      </listitem>
344     
345      <listitem>
346        <para>
347        The lower right shows a list of warnings and error
348        messages that was found when validating the experiment.
349        <nohelp>
350        In the example you can see that we have failed to
351        specify a value for the <guilabel>Temperature</guilabel>
352        protocol parameter for one of the samples.
353        </nohelp>
354        </para>
355      </listitem>
356       
357      <listitem>
358        <para>
359          The upper right shows information about the
360          currently selected item in the tree. This part also
361          contains more information errors or warnings for this
362          item. It may also present you with one or more suggestions
363          about how to fix the problem and with a link that
364          takes you to the most probable location where you can fix
365          the error or warning.
366        </para>
367       
368        <note>
369          <title>No links?</title>
370          If you don't have permission to change things no links
371          will be shown.
372        </note>
373       
374      </listitem>
375       
376    </itemizedlist>
377   
378    <seeother>
379      <other external_id="experiment.overview.validationoptions"
380        >Validation options</other>
381      <other external_id="experiment.overview.fixfailures"
382        >How to fix validation failures</other>
383    </seeother>
384   
385    </helptext>
386   
387    <sect3 id="experiments_analysis.validationoptions">
388      <title>Validation options</title>
389      <para>
390        Click on the <guibutton>Validation options</guibutton>
391        button in the toolbar to open the <guilabel>Validation
392        options</guilabel> dialog.
393      </para>
394     
395      <figure id="experiments_analysis.figures.validationoptions">
396        <title>Validation options</title>
397        <screenshot>
398          <mediaobject>
399            <imageobject><imagedata 
400              fileref="figures/validation_options.png" format="PNG"
401              /></imageobject>
402          </mediaobject>
403        </screenshot>
404      </figure>         
405     
406      <helptext external_id="experiment.overview.validationoptions" 
407        title="Validation options">
408        <para>
409          The validation procedure is highly
410          configurable and you can select what you want to
411          ignore, or something should be displayed as an error
412          or warning.
413        </para>
414       
415        <variablelist>
416          <varlistentry>
417            <term>
418            <indexterm><primary>Presets</primary><secondary>experiment validation</secondary></indexterm>
419            <guilabel>Presets</guilabel></term>
420            <listitem>
421              <para>
422              The list contains predefined and
423              user defined validation options.
424              Use the <guibutton>Save as&hellip;</guibutton>
425              button to save the current options as a user defined
426              preset. The <guibutton>Remove&hellip;</guibutton>
427              button is used to remove the currently selected
428              preset. Predefined presets can't be deleted.
429              </para>
430            </listitem>
431          </varlistentry>
432         
433          <varlistentry>
434            <term><guilabel>Project defaults</guilabel></term>
435            <listitem>
436              <para>
437              The options in this section are used to check
438              if your experiment uses the same values as set
439              by the project default values of the currently active
440              project<nohelp>
441              (see <xref linkend="project_permission.projects" />)</nohelp>.
442              If no project is active or if the active project doesn't
443              have default values these options are ignored.
444              </para>
445            </listitem>
446           
447          </varlistentry>
448         
449          <varlistentry>
450            <term><guilabel>Missing items</guilabel></term>
451            <listitem>
452              <para>
453              The options in this section are used to check if
454              you have specified values for optional items.
455              For example, there is an option that warns you if
456              you havn't specified a protocol.
457              </para>
458            </listitem>
459          </varlistentry>
460         
461          <varlistentry>
462            <term><guilabel>Annotations</guilabel></term>
463            <listitem>
464              <para>
465              The options in this section are used to check
466              problems related to annotations. The most
467              important ones are listed here:
468              </para>
469             
470              <itemizedlist>
471              <listitem>
472                <simpara>
473                <emphasis>Missing MIAME annotation value</emphasis>:
474                Checks that you have specified values
475                for all annotations marked as
476                <guilabel>Required for MIAME</guilabel>.
477                </simpara>
478              </listitem>
479             
480              <listitem>
481                <simpara>
482                <emphasis>Missing factor value</emphasis>:
483                Checks that you have specified values for
484                all annotations used as experimental factors in
485                the experiment.
486                </simpara>
487              </listitem>
488             
489              <listitem>
490                <simpara>
491                <emphasis>Missing parameter value</emphasis>:
492                Checks that you have specified values
493                for all protocol parameters.
494                </simpara>
495              </listitem>
496
497              <listitem>
498                <simpara>
499                <emphasis>Annotation is protocol parameter</emphasis>:
500                Checks if an item has been annotated with a
501                an annotation that is actually a protocol parameter.
502                </simpara>
503              </listitem>
504
505              <listitem>
506                <simpara>
507                <emphasis>Annotation has invalid value</emphasis>:
508                Checks if annotation values are correct with
509                respect to the rules given by the annotation type.
510                This might include numeric values that are outside
511                the valid range, or values not in the list
512                of allows values for an enumerated annotation type.
513                </simpara>
514              </listitem>
515
516              <listitem>
517                <simpara>
518                <emphasis>Inheriting annotation from non-parent</emphasis>:
519                Checks if inherited annotations really comes from a
520                parent item. This might happen if you rearrange
521                parent-child relationship because you found that
522                they were incorrectly linked.
523                </simpara>
524              </listitem>
525              </itemizedlist>
526             
527           
528            </listitem>
529          </varlistentry>
530         
531          <varlistentry>
532            <term><guilabel>Denied access</guilabel></term>
533            <listitem>
534              <para>
535              The options in this section are used to
536              check if you don't have access (read permission)
537              to an item in the experiment hierarchy. If this
538              happens the validation can't proceed in that branch.
539              This might mask other validation problems.
540              </para>
541            </listitem>
542          </varlistentry>
543         
544          <varlistentry>
545            <term><guilabel>Other</guilabel></term>
546            <listitem>
547              <para>
548              This section collects options that doesn't fit
549              into any of the other sections. The most
550              important options are:
551              </para>
552             
553              <itemizedlist>
554                <listitem>
555                  <simpara>
556                  <emphasis>Array deign mismatch</emphasis>:
557                  Checks if the array design specified for
558                  a raw bioassay is the same array design
559                  specified for the hybridization.
560                  </simpara>
561                </listitem>
562               
563                <listitem>
564                  <simpara>
565                  <emphasis>Multiple array designs</emphasis>:
566                  Checks if all raw bioassays use the
567                  same array design or not.
568                  </simpara>
569                </listitem>
570             
571                <listitem>
572                  <simpara>
573                  <emphasis>Incorrect number of labled extracts</emphasis>:
574                  Checks if the number of labeled extracts
575                  match the number of channels for the experiment.
576                  </simpara>
577                </listitem>
578
579                <listitem>
580                  <simpara>
581                  <emphasis>Non-unique name</emphasis>:
582                  Checks if two items of the same type
583                  have the same name. A unique name if important
584                  when exporting data in Tab2Mage format.
585                  </simpara>
586                </listitem>
587
588                <listitem>
589                  <simpara>
590                  <emphasis>Circular reference to pooled item</emphasis>:
591                  If you have used pooling, checks that no
592                  circular references have been created.
593                  </simpara>
594                </listitem>
595             
596              </itemizedlist>
597             
598            </listitem>
599          </varlistentry>
600         
601        </variablelist>
602       
603        <para>
604          Click on the &gbSave; button
605          to use the current settings. The display will
606          automatically refresh itself.
607        </para>
608       
609      </helptext>
610     
611      <helptext external_id="experiment.overview.validationoptions.savepreset" 
612        title="Save preset" webonly="1">
613       
614        <para>
615        Saves all validation options as a preset.
616        </para>
617       
618        <variablelist>
619          <varlistentry>
620            <term><guilabel>Name</guilabel></term>
621            <listitem>
622              <para>
623                The name of the preset. The name must be unique
624                and if a preset with the same name already exists
625                you will be asked if you want to overwrite it or not.
626              </para>
627            </listitem>
628          </varlistentry>
629        </variablelist>
630       
631        <para>
632          Click on the &gbSave; button
633          to save the preset or &gbCancel;
634          to abort.
635        </para>
636      </helptext>
637     
638    </sect3>
639   
640    <sect3 id="experiments_analysis.fixfailures">
641      <title>Fixing validation failures</title>
642      <helptext external_id="experiment.overview.fixfailures" 
643        title="How to fix validation failures">
644       
645        <para>
646        The experiment overview includes a function that allows
647        you to quickly fix most of the problems found during the
648        validation. The easiest way to use the function is:
649        </para>
650       
651        <orderedlist>
652          <listitem>
653            <simpara>
654            Click on an error or warning in the list of failures in
655            the lower right
656            pane. The tree in the left pane and the item overview in the
657            top right pane will automatically be updated to show the
658            exact location of the faulty item.
659            </simpara>
660          </listitem>
661          <listitem>
662            <simpara>
663            The upper right pane should contain a list labeled
664            <guilabel>Failure details</guilabel> with more information
665            about each failure and also one or more suggestions for fixing
666            the problem. For example, a failure due to a missing item
667            should suggest that you add or select an item.
668            </simpara>
669          </listitem>
670         
671          <listitem>
672            <simpara>
673            The suggestions should also have links that takes
674            you to an edit view where you can do the changes.
675            </simpara>
676          </listitem>
677         
678          <listitem>
679            <simpara>
680            After saving the changes you must click on the
681            <guibutton>Revalidate</guibutton> button to update
682            interface. If you want, you can fix more than one
683            failure before clicking on the button.
684            </simpara>
685          </listitem>
686           
687        </orderedlist>
688     
689      </helptext>
690    </sect3>
691   
692  </sect2>
693 
694  <sect2 id="experiments_analysis.magexport">
695    <title>Tab2Mage export</title>
696    <para>
697      <ulink url="http://tab2mage.sourceforge.net/"
698      >Tab2Mage format</ulink> is a tab-delimited format veted by
699      <ulink url="http://www.ebi.ac.uk/microarray/"
700      >EBI's ArrayExpress</ulink>
701      repository for submission microarray data.
702      Tab2Mage format has been chosen by BASE to provide an
703      easy way for data deposition to public repository when
704      submitting a manuscript and publishing experimental
705      data.
706    </para>
707     
708    <para>
709      BASE2 has been engineered to closely map the MIAME
710      concepts and a number of BASE2 entities can be mapped
711      directly to Tab2Mage elements. However, since MIAME is
712      focused on microarray processing workflow, information
713      about the biological sample is down to the user. To
714      accomodate the annotation needs of users, BASE2 provides
715      a mechanism that allows annotation customization to meet
716      user specific requirements. BASE allows to create
717      annotation type for quantitative annotation and
718      qualitative annotation
719    </para>     
720
721    <para>
722      BASE2 can export an experiment to Tab2Mage
723      format thanks to a dedicated export plug-in.
724      For the plug-in to work, it is important to understand that
725      information recorded in BASE should be
726      formatted following a small number of rules. Failing to
727      do so may impair the possibility of exporting to
728      ArrayExpress.
729    </para>
730   
731    <note>
732      <para>
733      The Tab2Mage export plug-in has not yet been included in the main
734      distribution. Hopefully, it will appear in the next (2.4) release.
735      </para>
736    </note>
737
738    <sect3 id="experiments_analysis.magexport.annotations">
739      <title>Biomaterial annotations</title>
740      <para>
741        Tab2Mage specifications only allow <emphasis>BioSource</emphasis>
742        items to be annotated with <emphasis>BioMaterialCharacteristics</emphasis>.
743      </para>
744      <warning>
745        <para>
746          All BASE2 Annotation Types used to annotate at
747          the level of <emphasis>Sample</emphasis> and
748          <emphasis>Extract</emphasis> items will
749          be lost during the export in Tab2Mage format in
750          order to comply with the ArrayExpress Tab2Mage
751          parser.
752        </para>
753      </warning>
754      <note>
755        <para>
756          In the context of data exchange between BASE
757          instances, the export function can be altered to
758          allow attachement of annotations to items
759          other than biosources, therefore avoiding loss of
760          information.
761        </para>
762      </note>
763    </sect3>
764
765    <sect3 id="experiments_analysis.magexport.units">
766      <title>Annotation units</title>
767      <para>
768        To associate units to BASE2 annotation types and
769        remain compatible with Tab2Mage specifications,
770        users need to adhere to the following convention:
771      </para>
772      <para>
773        <userinput>annotation_type_name(unit_name)</userinput> as in
774        <userinput>body mass(kg)</userinput> or <userinput>concentration(mg/ml)</userinput>
775      </para>
776      <warning>
777        <para>
778          Only one unit can be specified at any one time
779          for any given annotation type. In order to
780          enable Tab2Mage support, it might be necessary
781          to declare several related Annotation Type in
782          order to report similar kind of information but
783          expressed in a different unit. Specifying Age
784          for instance is a good example on how to deal
785          with such cases: One should create several
786          related annotation types e.g. <userinput>Age(week)</userinput>,
787          <userinput>Age(year)</userinput> or <userinput>Age(month)</userinput> 
788          as those variations maybe be necessary when reporting the age of a
789          mouse or the age of a human volunteer.
790        </para>
791      </warning>
792    </sect3>
793    <sect3
794      id="experiments_analysis.magexport.parameters">
795      <title>Protocol parameters</title>
796      <para>
797        In order to ensure MIAME compliance, Tab2Mage
798        specifications cater for reporting parameters
799        attached to protocols and all parameters attached to
800        a protocol should be declared in the protocol
801        section of a Tab2Mage file.
802      </para>
803     
804      <para>
805        In BASE2 terms, Tab2Mage elements such as
806        <emphasis>BioMaterialCharacteristics</emphasis>,
807        <emphasis>Parameter</emphasis> or
808        <emphasis>FactorValues</emphasis> are all annotation
809        types. But, it is necessary to flag those annotations types meant to
810        be used as protocol parameters as such so that they
811        can identified by the Tab2Mage exporter and handled
812        appropriately.
813      </para>
814
815      <warning>
816        <para>
817          It is not possible to use the same
818          annotation type <emphasis>Temperature</emphasis> for reporting a
819          patient body temperature (which is a
820          <emphasis>Biomaterial Characteristic</emphasis>) and hybridization
821          temperature (which is a protocol parameter).
822          Hence it will be necessary to declare 2 distinct
823          annotation types:
824        </para>
825      </warning>
826     
827      <itemizedlist>
828      <listitem>
829        <para>
830        Annotation type to be used as <emphasis>BioSource
831          characteristics</emphasis>: <userinput>body temperature (degree_C)</userinput>
832        </para>
833      </listitem>
834      <listitem>
835        <para>
836        Annotation type to be used as <emphasis>protocol parameter</emphasis>:
837        <userinput>hybridization temperature (degree_C)</userinput>
838        </para>
839      </listitem>
840      </itemizedlist>
841    </sect3>
842         
843    <sect3 id="experiments_analysis.magexport.factors">
844      <title>Experimental factors</title>
845      <para>
846        It is a MIAME requirement to identify <emphasis>Experimental
847        Variables</emphasis> when submitting data to ArrayExpress
848        (provided the study is an intervention study).
849        Therefore, BASE2 users willing to use the Tab2Mage
850        export function will have to declare <emphasis>Experimental
851        Factors</emphasis> using the the <guilabel>Experimental Factor</guilabel>
852        tab available when editing experiments. See
853        <xref linkend="experiments_analysis.experiment.factors" /> for more information.
854      </para>
855     
856      <para>
857        Values for the experimental factors are take from annotations.
858        The annotation must exist at the raw bioassay level, which
859        probably means that you have to inherit the annotation from
860        some other item, for example, a biosource or a sample.
861        It is also possible to use a protocol parameter as
862        experimental factor. See <xref linkend="annotations" /> for
863        more information about annotations.
864      </para>
865    </sect3>
866  </sect2>
867</sect1>
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