source: trunk/doc/src/docbook/userdoc/experiments.xml @ 3423

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Fixed image scaling issues in the PDF version

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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 or biosource level the raw bioassays
275        must inherit those annotations.
276        <nohelp>Read <xref linkend="annotations.inheriting" /> 
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    <helptext external_id="experiment.overview" 
304      title="Experiment overview">
305   
306    <para>
307      With the <guilabel>Experiment overview</guilabel> 
308      function you can get an overview of all hybridizations,
309      extracts, samples, annotations, etc. used in an
310      experiment. The overview includes a lot of checks
311      that validates your experimental setup for missing
312      or possibly incorrect information.
313    </para>
314   
315    <nohelp>
316    <para>
317      You can access the overview of an experiment by navigating
318      to the single-item view of the experiment you are interested in.
319      Then, switch to the <guilabel>Overview</guilabel> tab that
320      is present on that page. Here is an example of what is displayed:
321    </para>
322   
323    <figure id="experiments_analysis.figures.experimentoverview">
324      <title>The experiment overview</title>
325      <screenshot>
326        <mediaobject>
327          <imageobject><imagedata 
328            scalefit="1" width="100%"
329            fileref="figures/experiment_overview.png" format="PNG"
330            /></imageobject>
331        </mediaobject>
332      </screenshot>
333    </figure>
334    </nohelp>
335   
336    <para>
337      The page is divided into three sections:
338    </para>
339   
340    <itemizedlist>
341      <listitem>
342        <para>
343        To the left is a tree displaying all items
344        in the experiment and how they are linked to
345        each other.
346        </para>
347      </listitem>
348     
349      <listitem>
350        <para>
351        The lower right shows a list of warnings and error
352        messages that was found when validating the experiment.
353        <nohelp>
354        In the example you can see that we have failed to
355        specify a value for the <guilabel>Temperature</guilabel>
356        protocol parameter for one of the samples.
357        </nohelp>
358        </para>
359      </listitem>
360       
361      <listitem>
362        <para>
363          The upper right shows information about the
364          currently selected item in the tree. This part also
365          contains more information errors or warnings for this
366          item. It may also present you with one or more suggestions
367          about how to fix the problem and with a link that
368          takes you to the most probable location where you can fix
369          the error or warning.
370        </para>
371       
372        <note>
373          <title>No links?</title>
374          If you don't have permission to change things no links
375          will be shown.
376        </note>
377       
378      </listitem>
379       
380    </itemizedlist>
381   
382    <seeother>
383      <other external_id="experiment.overview.validationoptions"
384        >Validation options</other>
385      <other external_id="experiment.overview.fixfailures"
386        >How to fix validation failures</other>
387    </seeother>
388   
389    </helptext>
390   
391    <sect3 id="experiments_analysis.validationoptions">
392      <title>Validation options</title>
393      <para>
394        Click on the <guibutton>Validation options</guibutton>
395        button in the toolbar to open the <guilabel>Validation
396        options</guilabel> dialog.
397      </para>
398     
399      <figure id="experiments_analysis.figures.validationoptions">
400        <title>Validation options</title>
401        <screenshot>
402          <mediaobject>
403            <imageobject><imagedata 
404              fileref="figures/validation_options.png" format="PNG"
405              /></imageobject>
406          </mediaobject>
407        </screenshot>
408      </figure>         
409     
410      <helptext external_id="experiment.overview.validationoptions" 
411        title="Validation options">
412        <para>
413          The validation procedure is highly
414          configurable and you can select what you want to
415          ignore, or something should be displayed as an error
416          or warning.
417        </para>
418       
419        <variablelist>
420          <varlistentry>
421            <term>
422            <guilabel>Presets</guilabel></term>
423            <listitem>
424              <para>
425              The list contains predefined and
426              user defined validation options.
427              Use the <guibutton>Save as&hellip;</guibutton>
428              button to save the current options as a user defined
429              preset. The <guibutton>Remove&hellip;</guibutton>
430              button is used to remove the currently selected
431              preset. Predefined presets can't be deleted.
432              </para>
433            </listitem>
434          </varlistentry>
435         
436          <varlistentry>
437            <term><guilabel>Project defaults</guilabel></term>
438            <listitem>
439              <para>
440              The options in this section are used to check
441              if your experiment uses the same values as set
442              by the project default values of the currently active
443              project<nohelp>
444              (see <xref linkend="project_permission.projects" />)</nohelp>.
445              If no project is active or if the active project doesn't
446              have default values these options are ignored.
447              </para>
448            </listitem>
449           
450          </varlistentry>
451         
452          <varlistentry>
453            <term><guilabel>Missing items</guilabel></term>
454            <listitem>
455              <para>
456              The options in this section are used to check if
457              you have specified values for optional items.
458              For example, there is an option that warns you if
459              you havn't specified a protocol.
460              </para>
461            </listitem>
462          </varlistentry>
463         
464          <varlistentry>
465            <term><guilabel>Annotations</guilabel></term>
466            <listitem>
467              <para>
468              The options in this section are used to check
469              problems related to annotations. The most
470              important ones are listed here:
471              </para>
472             
473              <itemizedlist>
474              <listitem>
475                <simpara>
476                <emphasis>Missing MIAME annotation value</emphasis>:
477                Checks that you have specified values
478                for all annotations marked as
479                <guilabel>Required for MIAME</guilabel>.
480                </simpara>
481              </listitem>
482             
483              <listitem>
484                <simpara>
485                <emphasis>Missing factor value</emphasis>:
486                Checks that you have specified values for
487                all annotations used as experimental factors in
488                the experiment.
489                </simpara>
490              </listitem>
491             
492              <listitem>
493                <simpara>
494                <emphasis>Missing parameter value</emphasis>:
495                Checks that you have specified values
496                for all protocol parameters.
497                </simpara>
498              </listitem>
499
500              <listitem>
501                <simpara>
502                <emphasis>Annotation is protocol parameter</emphasis>:
503                Checks if an item has been annotated with a
504                an annotation that is actually a protocol parameter.
505                </simpara>
506              </listitem>
507
508              <listitem>
509                <simpara>
510                <emphasis>Annotation has invalid value</emphasis>:
511                Checks if annotation values are correct with
512                respect to the rules given by the annotation type.
513                This might include numeric values that are outside
514                the valid range, or values not in the list
515                of allows values for an enumerated annotation type.
516                </simpara>
517              </listitem>
518
519              <listitem>
520                <simpara>
521                <emphasis>Inheriting annotation from non-parent</emphasis>:
522                Checks if inherited annotations really comes from a
523                parent item. This might happen if you rearrange
524                parent-child relationship because you found that
525                they were incorrectly linked.
526                </simpara>
527              </listitem>
528              </itemizedlist>
529             
530           
531            </listitem>
532          </varlistentry>
533         
534          <varlistentry>
535            <term><guilabel>Denied access</guilabel></term>
536            <listitem>
537              <para>
538              The options in this section are used to
539              check if you don't have access (read permission)
540              to an item in the experiment hierarchy. If this
541              happens the validation can't proceed in that branch.
542              This might mask other validation problems.
543              </para>
544            </listitem>
545          </varlistentry>
546         
547          <varlistentry>
548            <term><guilabel>Other</guilabel></term>
549            <listitem>
550              <para>
551              This section collects options that doesn't fit
552              into any of the other sections. The most
553              important options are:
554              </para>
555             
556              <itemizedlist>
557                <listitem>
558                  <simpara>
559                  <emphasis>Array deign mismatch</emphasis>:
560                  Checks if the array design specified for
561                  a raw bioassay is the same array design
562                  specified for the hybridization.
563                  </simpara>
564                </listitem>
565               
566                <listitem>
567                  <simpara>
568                  <emphasis>Multiple array designs</emphasis>:
569                  Checks if all raw bioassays use the
570                  same array design or not.
571                  </simpara>
572                </listitem>
573             
574                <listitem>
575                  <simpara>
576                  <emphasis>Incorrect number of labled extracts</emphasis>:
577                  Checks if the number of labeled extracts
578                  match the number of channels for the experiment.
579                  </simpara>
580                </listitem>
581
582                <listitem>
583                  <simpara>
584                  <emphasis>Non-unique name</emphasis>:
585                  Checks if two items of the same type
586                  have the same name. A unique name if important
587                  when exporting data in Tab2Mage format.
588                  </simpara>
589                </listitem>
590
591                <listitem>
592                  <simpara>
593                  <emphasis>Circular reference to pooled item</emphasis>:
594                  If you have used pooling, checks that no
595                  circular references have been created.
596                  </simpara>
597                </listitem>
598             
599              </itemizedlist>
600             
601            </listitem>
602          </varlistentry>
603         
604        </variablelist>
605       
606        <para>
607          Click on the &gbSave; button
608          to use the current settings. The display will
609          automatically refresh itself.
610        </para>
611       
612      </helptext>
613     
614      <helptext external_id="experiment.overview.validationoptions.savepreset" 
615        title="Save preset" webonly="1">
616       
617        <para>
618        Saves all validation options as a preset.
619        </para>
620       
621        <variablelist>
622          <varlistentry>
623            <term><guilabel>Name</guilabel></term>
624            <listitem>
625              <para>
626                The name of the preset. The name must be unique
627                and if a preset with the same name already exists
628                you will be asked if you want to overwrite it or not.
629              </para>
630            </listitem>
631          </varlistentry>
632        </variablelist>
633       
634        <para>
635          Click on the &gbSave; button
636          to save the preset or &gbCancel;
637          to abort.
638        </para>
639      </helptext>
640     
641    </sect3>
642   
643    <sect3 id="experiments_analysis.fixfailures">
644      <title>Fixing validation failures</title>
645      <helptext external_id="experiment.overview.fixfailures" 
646        title="How to fix validation failures">
647       
648        <para>
649        The experiment overview includes a function that allows
650        you to quickly fix most of the problems found during the
651        validation. The easiest way to use the function is:
652        </para>
653       
654        <orderedlist>
655          <listitem>
656            <simpara>
657            Click on an error or warning in the list of failures in
658            the lower right
659            pane. The tree in the left pane and the item overview in the
660            top right pane will automatically be updated to show the
661            exact location of the faulty item.
662            </simpara>
663          </listitem>
664          <listitem>
665            <simpara>
666            The upper right pane should contain a list labeled
667            <guilabel>Failure details</guilabel> with more information
668            about each failure and also one or more suggestions for fixing
669            the problem. For example, a failure due to a missing item
670            should suggest that you add or select an item.
671            </simpara>
672          </listitem>
673         
674          <listitem>
675            <simpara>
676            The suggestions should also have links that takes
677            you to an edit view where you can do the changes.
678            </simpara>
679          </listitem>
680         
681          <listitem>
682            <simpara>
683            After saving the changes you must click on the
684            <guibutton>Revalidate</guibutton> button to update
685            interface. If you want, you can fix more than one
686            failure before clicking on the button.
687            </simpara>
688          </listitem>
689           
690        </orderedlist>
691     
692      </helptext>
693    </sect3>
694   
695  </sect2>
696 
697  <sect2 id="experiments_analysis.magexport">
698    <title>Tab2Mage export</title>
699    <para>
700      <ulink url="http://tab2mage.sourceforge.net/"
701      >Tab2Mage format</ulink> is a tab-delimited format veted by
702      <ulink url="http://www.ebi.ac.uk/microarray/"
703      >EBI's ArrayExpress</ulink>
704      repository for submission microarray data.
705      Tab2Mage format has been chosen by BASE to provide an
706      easy way for data deposition to public repository when
707      submitting a manuscript and publishing experimental
708      data.
709    </para>
710     
711    <para>
712      BASE2 has been engineered to closely map the MIAME
713      concepts and a number of BASE2 entities can be mapped
714      directly to Tab2Mage elements. However, since MIAME is
715      focused on microarray processing workflow, information
716      about the biological sample is down to the user. To
717      accomodate the annotation needs of users, BASE2 provides
718      a mechanism that allows annotation customization to meet
719      user specific requirements. BASE allows to create
720      annotation type for quantitative annotation and
721      qualitative annotation
722    </para>     
723
724    <para>
725      BASE2 can export an experiment to Tab2Mage
726      format thanks to a dedicated export plug-in.
727      For the plug-in to work, it is important to understand that
728      information recorded in BASE should be
729      formatted following a small number of rules. Failing to
730      do so may impair the possibility of exporting to
731      ArrayExpress.
732    </para>
733   
734    <note>
735      <para>
736      The Tab2Mage export plug-in has not yet been included in the main
737      distribution. Hopefully, it will appear in the next (2.4) release.
738      </para>
739    </note>
740
741    <sect3 id="experiments_analysis.magexport.annotations">
742      <title>Biomaterial annotations</title>
743      <para>
744        Tab2Mage specifications only allow <emphasis>BioSource</emphasis>
745        items to be annotated with <emphasis>BioMaterialCharacteristics</emphasis>.
746      </para>
747      <warning>
748        <para>
749          All BASE2 Annotation Types used to annotate at
750          the level of <emphasis>Sample</emphasis> and
751          <emphasis>Extract</emphasis> items will
752          be lost during the export in Tab2Mage format in
753          order to comply with the ArrayExpress Tab2Mage
754          parser.
755        </para>
756      </warning>
757      <note>
758        <para>
759          In the context of data exchange between BASE
760          instances, the export function can be altered to
761          allow attachement of annotations to items
762          other than biosources, therefore avoiding loss of
763          information.
764        </para>
765      </note>
766    </sect3>
767
768    <sect3 id="experiments_analysis.magexport.units">
769      <title>Annotation units</title>
770      <para>
771        To associate units to BASE2 annotation types and
772        remain compatible with Tab2Mage specifications,
773        users need to adhere to the following convention:
774      </para>
775      <para>
776        <userinput>annotation_type_name(unit_name)</userinput> as in
777        <userinput>body mass(kg)</userinput> or <userinput>concentration(mg/ml)</userinput>
778      </para>
779      <warning>
780        <para>
781          Only one unit can be specified at any one time
782          for any given annotation type. In order to
783          enable Tab2Mage support, it might be necessary
784          to declare several related Annotation Type in
785          order to report similar kind of information but
786          expressed in a different unit. Specifying Age
787          for instance is a good example on how to deal
788          with such cases: One should create several
789          related annotation types e.g. <userinput>Age(week)</userinput>,
790          <userinput>Age(year)</userinput> or <userinput>Age(month)</userinput> 
791          as those variations maybe be necessary when reporting the age of a
792          mouse or the age of a human volunteer.
793        </para>
794      </warning>
795    </sect3>
796    <sect3
797      id="experiments_analysis.magexport.parameters">
798      <title>Protocol parameters</title>
799      <para>
800        In order to ensure MIAME compliance, Tab2Mage
801        specifications cater for reporting parameters
802        attached to protocols and all parameters attached to
803        a protocol should be declared in the protocol
804        section of a Tab2Mage file.
805      </para>
806     
807      <para>
808        In BASE2 terms, Tab2Mage elements such as
809        <emphasis>BioMaterialCharacteristics</emphasis>,
810        <emphasis>Parameter</emphasis> or
811        <emphasis>FactorValues</emphasis> are all annotation
812        types. But, it is necessary to flag those annotations types meant to
813        be used as protocol parameters as such so that they
814        can identified by the Tab2Mage exporter and handled
815        appropriately.
816      </para>
817
818      <warning>
819        <para>
820          It is not possible to use the same
821          annotation type <emphasis>Temperature</emphasis> for reporting a
822          patient body temperature (which is a
823          <emphasis>Biomaterial Characteristic</emphasis>) and hybridization
824          temperature (which is a protocol parameter).
825          Hence it will be necessary to declare 2 distinct
826          annotation types:
827        </para>
828      </warning>
829     
830      <itemizedlist>
831      <listitem>
832        <para>
833        Annotation type to be used as <emphasis>BioSource
834          characteristics</emphasis>: <userinput>body temperature (degree_C)</userinput>
835        </para>
836      </listitem>
837      <listitem>
838        <para>
839        Annotation type to be used as <emphasis>protocol parameter</emphasis>:
840        <userinput>hybridization temperature (degree_C)</userinput>
841        </para>
842      </listitem>
843      </itemizedlist>
844    </sect3>
845         
846    <sect3 id="experiments_analysis.magexport.factors">
847      <title>Experimental factors</title>
848      <para>
849        It is a MIAME requirement to identify <emphasis>Experimental
850        Variables</emphasis> when submitting data to ArrayExpress
851        (provided the study is an intervention study).
852        Therefore, BASE2 users willing to use the Tab2Mage
853        export function will have to declare <emphasis>Experimental
854        Factors</emphasis> using the the <guilabel>Experimental Factor</guilabel>
855        tab available when editing experiments. See
856        <xref linkend="experiments_analysis.experiment.factors" /> for more information.
857      </para>
858     
859      <para>
860        Values for the experimental factors are take from annotations.
861        The annotation must exist at the raw bioassay level, which
862        probably means that you have to inherit the annotation from
863        some other item, for example, a biosource or a sample.
864        It is also possible to use a protocol parameter as
865        experimental factor. See <xref linkend="annotations" /> for
866        more information about annotations.
867      </para>
868    </sect3>
869  </sect2>
870</sect1>
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