source: trunk/doc/src/docbook/userdoc/experiments.xml @ 3400

Last change on this file since 3400 was 3400, checked in by Nicklas Nordborg, 14 years ago

Fixes #534.

File size: 27.0 KB
Line 
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            fileref="figures/experiment_overview.png" format="PNG"
329            /></imageobject>
330        </mediaobject>
331      </screenshot>
332    </figure>
333    </nohelp>
334   
335    <para>
336      The page is divided into three sections:
337    </para>
338   
339    <itemizedlist>
340      <listitem>
341        <para>
342        To the left is a tree displaying all items
343        in the experiment and how they are linked to
344        each other.
345        </para>
346      </listitem>
347     
348      <listitem>
349        <para>
350        The lower right shows a list of warnings and error
351        messages that was found when validating the experiment.
352        <nohelp>
353        In the example you can see that we have failed to
354        specify a value for the <guilabel>Temperature</guilabel>
355        protocol parameter for one of the samples.
356        </nohelp>
357        </para>
358      </listitem>
359       
360      <listitem>
361        <para>
362          The upper right shows information about the
363          currently selected item in the tree. This part also
364          contains more information errors or warnings for this
365          item. It may also present you with one or more suggestions
366          about how to fix the problem and with a link that
367          takes you to the most probable location where you can fix
368          the error or warning.
369        </para>
370       
371        <note>
372          <title>No links?</title>
373          If you don't have permission to change things no links
374          will be shown.
375        </note>
376       
377      </listitem>
378       
379    </itemizedlist>
380   
381    <seeother>
382      <other external_id="experiment.overview.validationoptions"
383        >Validation options</other>
384      <other external_id="experiment.overview.fixfailures"
385        >How to fix validation failures</other>
386    </seeother>
387   
388    </helptext>
389   
390    <sect3 id="experiments_analysis.validationoptions">
391      <title>Validation options</title>
392      <para>
393        Click on the <guibutton>Validation options</guibutton>
394        button in the toolbar to open the <guilabel>Validation
395        options</guilabel> dialog.
396      </para>
397     
398      <figure id="experiments_analysis.figures.validationoptions">
399        <title>Validation options</title>
400        <screenshot>
401          <mediaobject>
402            <imageobject><imagedata 
403              fileref="figures/validation_options.png" format="PNG"
404              /></imageobject>
405          </mediaobject>
406        </screenshot>
407      </figure>         
408     
409      <helptext external_id="experiment.overview.validationoptions" 
410        title="Validation options">
411        <para>
412          The validation procedure is highly
413          configurable and you can select what you want to
414          ignore, or something should be displayed as an error
415          or warning.
416        </para>
417       
418        <variablelist>
419          <varlistentry>
420            <term>
421            <guilabel>Presets</guilabel></term>
422            <listitem>
423              <para>
424              The list contains predefined and
425              user defined validation options.
426              Use the <guibutton>Save as&hellip;</guibutton>
427              button to save the current options as a user defined
428              preset. The <guibutton>Remove&hellip;</guibutton>
429              button is used to remove the currently selected
430              preset. Predefined presets can't be deleted.
431              </para>
432            </listitem>
433          </varlistentry>
434         
435          <varlistentry>
436            <term><guilabel>Project defaults</guilabel></term>
437            <listitem>
438              <para>
439              The options in this section are used to check
440              if your experiment uses the same values as set
441              by the project default values of the currently active
442              project<nohelp>
443              (see <xref linkend="project_permission.projects" />)</nohelp>.
444              If no project is active or if the active project doesn't
445              have default values these options are ignored.
446              </para>
447            </listitem>
448           
449          </varlistentry>
450         
451          <varlistentry>
452            <term><guilabel>Missing items</guilabel></term>
453            <listitem>
454              <para>
455              The options in this section are used to check if
456              you have specified values for optional items.
457              For example, there is an option that warns you if
458              you havn't specified a protocol.
459              </para>
460            </listitem>
461          </varlistentry>
462         
463          <varlistentry>
464            <term><guilabel>Annotations</guilabel></term>
465            <listitem>
466              <para>
467              The options in this section are used to check
468              problems related to annotations. The most
469              important ones are listed here:
470              </para>
471             
472              <itemizedlist>
473              <listitem>
474                <simpara>
475                <emphasis>Missing MIAME annotation value</emphasis>:
476                Checks that you have specified values
477                for all annotations marked as
478                <guilabel>Required for MIAME</guilabel>.
479                </simpara>
480              </listitem>
481             
482              <listitem>
483                <simpara>
484                <emphasis>Missing factor value</emphasis>:
485                Checks that you have specified values for
486                all annotations used as experimental factors in
487                the experiment.
488                </simpara>
489              </listitem>
490             
491              <listitem>
492                <simpara>
493                <emphasis>Missing parameter value</emphasis>:
494                Checks that you have specified values
495                for all protocol parameters.
496                </simpara>
497              </listitem>
498
499              <listitem>
500                <simpara>
501                <emphasis>Annotation is protocol parameter</emphasis>:
502                Checks if an item has been annotated with a
503                an annotation that is actually a protocol parameter.
504                </simpara>
505              </listitem>
506
507              <listitem>
508                <simpara>
509                <emphasis>Annotation has invalid value</emphasis>:
510                Checks if annotation values are correct with
511                respect to the rules given by the annotation type.
512                This might include numeric values that are outside
513                the valid range, or values not in the list
514                of allows values for an enumerated annotation type.
515                </simpara>
516              </listitem>
517
518              <listitem>
519                <simpara>
520                <emphasis>Inheriting annotation from non-parent</emphasis>:
521                Checks if inherited annotations really comes from a
522                parent item. This might happen if you rearrange
523                parent-child relationship because you found that
524                they were incorrectly linked.
525                </simpara>
526              </listitem>
527              </itemizedlist>
528             
529           
530            </listitem>
531          </varlistentry>
532         
533          <varlistentry>
534            <term><guilabel>Denied access</guilabel></term>
535            <listitem>
536              <para>
537              The options in this section are used to
538              check if you don't have access (read permission)
539              to an item in the experiment hierarchy. If this
540              happens the validation can't proceed in that branch.
541              This might mask other validation problems.
542              </para>
543            </listitem>
544          </varlistentry>
545         
546          <varlistentry>
547            <term><guilabel>Other</guilabel></term>
548            <listitem>
549              <para>
550              This section collects options that doesn't fit
551              into any of the other sections. The most
552              important options are:
553              </para>
554             
555              <itemizedlist>
556                <listitem>
557                  <simpara>
558                  <emphasis>Array deign mismatch</emphasis>:
559                  Checks if the array design specified for
560                  a raw bioassay is the same array design
561                  specified for the hybridization.
562                  </simpara>
563                </listitem>
564               
565                <listitem>
566                  <simpara>
567                  <emphasis>Multiple array designs</emphasis>:
568                  Checks if all raw bioassays use the
569                  same array design or not.
570                  </simpara>
571                </listitem>
572             
573                <listitem>
574                  <simpara>
575                  <emphasis>Incorrect number of labled extracts</emphasis>:
576                  Checks if the number of labeled extracts
577                  match the number of channels for the experiment.
578                  </simpara>
579                </listitem>
580
581                <listitem>
582                  <simpara>
583                  <emphasis>Non-unique name</emphasis>:
584                  Checks if two items of the same type
585                  have the same name. A unique name if important
586                  when exporting data in Tab2Mage format.
587                  </simpara>
588                </listitem>
589
590                <listitem>
591                  <simpara>
592                  <emphasis>Circular reference to pooled item</emphasis>:
593                  If you have used pooling, checks that no
594                  circular references have been created.
595                  </simpara>
596                </listitem>
597             
598              </itemizedlist>
599             
600            </listitem>
601          </varlistentry>
602         
603        </variablelist>
604       
605        <para>
606          Click on the &gbSave; button
607          to use the current settings. The display will
608          automatically refresh itself.
609        </para>
610       
611      </helptext>
612     
613      <helptext external_id="experiment.overview.validationoptions.savepreset" 
614        title="Save preset" webonly="1">
615       
616        <para>
617        Saves all validation options as a preset.
618        </para>
619       
620        <variablelist>
621          <varlistentry>
622            <term><guilabel>Name</guilabel></term>
623            <listitem>
624              <para>
625                The name of the preset. The name must be unique
626                and if a preset with the same name already exists
627                you will be asked if you want to overwrite it or not.
628              </para>
629            </listitem>
630          </varlistentry>
631        </variablelist>
632       
633        <para>
634          Click on the &gbSave; button
635          to save the preset or &gbCancel;
636          to abort.
637        </para>
638      </helptext>
639     
640    </sect3>
641   
642    <sect3 id="experiments_analysis.fixfailures">
643      <title>Fixing validation failures</title>
644      <helptext external_id="experiment.overview.fixfailures" 
645        title="How to fix validation failures">
646       
647        <para>
648        The experiment overview includes a function that allows
649        you to quickly fix most of the problems found during the
650        validation. The easiest way to use the function is:
651        </para>
652       
653        <orderedlist>
654          <listitem>
655            <simpara>
656            Click on an error or warning in the list of failures in
657            the lower right
658            pane. The tree in the left pane and the item overview in the
659            top right pane will automatically be updated to show the
660            exact location of the faulty item.
661            </simpara>
662          </listitem>
663          <listitem>
664            <simpara>
665            The upper right pane should contain a list labeled
666            <guilabel>Failure details</guilabel> with more information
667            about each failure and also one or more suggestions for fixing
668            the problem. For example, a failure due to a missing item
669            should suggest that you add or select an item.
670            </simpara>
671          </listitem>
672         
673          <listitem>
674            <simpara>
675            The suggestions should also have links that takes
676            you to an edit view where you can do the changes.
677            </simpara>
678          </listitem>
679         
680          <listitem>
681            <simpara>
682            After saving the changes you must click on the
683            <guibutton>Revalidate</guibutton> button to update
684            interface. If you want, you can fix more than one
685            failure before clicking on the button.
686            </simpara>
687          </listitem>
688           
689        </orderedlist>
690     
691      </helptext>
692    </sect3>
693   
694  </sect2>
695 
696  <sect2 id="experiments_analysis.magexport">
697    <title>Tab2Mage export</title>
698    <para>
699      <ulink url="http://tab2mage.sourceforge.net/"
700      >Tab2Mage format</ulink> is a tab-delimited format veted by
701      <ulink url="http://www.ebi.ac.uk/microarray/"
702      >EBI's ArrayExpress</ulink>
703      repository for submission microarray data.
704      Tab2Mage format has been chosen by BASE to provide an
705      easy way for data deposition to public repository when
706      submitting a manuscript and publishing experimental
707      data.
708    </para>
709     
710    <para>
711      BASE2 has been engineered to closely map the MIAME
712      concepts and a number of BASE2 entities can be mapped
713      directly to Tab2Mage elements. However, since MIAME is
714      focused on microarray processing workflow, information
715      about the biological sample is down to the user. To
716      accomodate the annotation needs of users, BASE2 provides
717      a mechanism that allows annotation customization to meet
718      user specific requirements. BASE allows to create
719      annotation type for quantitative annotation and
720      qualitative annotation
721    </para>     
722
723    <para>
724      BASE2 can export an experiment to Tab2Mage
725      format thanks to a dedicated export plug-in.
726      For the plug-in to work, it is important to understand that
727      information recorded in BASE should be
728      formatted following a small number of rules. Failing to
729      do so may impair the possibility of exporting to
730      ArrayExpress.
731    </para>
732   
733    <note>
734      <para>
735      The Tab2Mage export plug-in has not yet been included in the main
736      distribution. Hopefully, it will appear in the next (2.4) release.
737      </para>
738    </note>
739
740    <sect3 id="experiments_analysis.magexport.annotations">
741      <title>Biomaterial annotations</title>
742      <para>
743        Tab2Mage specifications only allow <emphasis>BioSource</emphasis>
744        items to be annotated with <emphasis>BioMaterialCharacteristics</emphasis>.
745      </para>
746      <warning>
747        <para>
748          All BASE2 Annotation Types used to annotate at
749          the level of <emphasis>Sample</emphasis> and
750          <emphasis>Extract</emphasis> items will
751          be lost during the export in Tab2Mage format in
752          order to comply with the ArrayExpress Tab2Mage
753          parser.
754        </para>
755      </warning>
756      <note>
757        <para>
758          In the context of data exchange between BASE
759          instances, the export function can be altered to
760          allow attachement of annotations to items
761          other than biosources, therefore avoiding loss of
762          information.
763        </para>
764      </note>
765    </sect3>
766
767    <sect3 id="experiments_analysis.magexport.units">
768      <title>Annotation units</title>
769      <para>
770        To associate units to BASE2 annotation types and
771        remain compatible with Tab2Mage specifications,
772        users need to adhere to the following convention:
773      </para>
774      <para>
775        <userinput>annotation_type_name(unit_name)</userinput> as in
776        <userinput>body mass(kg)</userinput> or <userinput>concentration(mg/ml)</userinput>
777      </para>
778      <warning>
779        <para>
780          Only one unit can be specified at any one time
781          for any given annotation type. In order to
782          enable Tab2Mage support, it might be necessary
783          to declare several related Annotation Type in
784          order to report similar kind of information but
785          expressed in a different unit. Specifying Age
786          for instance is a good example on how to deal
787          with such cases: One should create several
788          related annotation types e.g. <userinput>Age(week)</userinput>,
789          <userinput>Age(year)</userinput> or <userinput>Age(month)</userinput> 
790          as those variations maybe be necessary when reporting the age of a
791          mouse or the age of a human volunteer.
792        </para>
793      </warning>
794    </sect3>
795    <sect3
796      id="experiments_analysis.magexport.parameters">
797      <title>Protocol parameters</title>
798      <para>
799        In order to ensure MIAME compliance, Tab2Mage
800        specifications cater for reporting parameters
801        attached to protocols and all parameters attached to
802        a protocol should be declared in the protocol
803        section of a Tab2Mage file.
804      </para>
805     
806      <para>
807        In BASE2 terms, Tab2Mage elements such as
808        <emphasis>BioMaterialCharacteristics</emphasis>,
809        <emphasis>Parameter</emphasis> or
810        <emphasis>FactorValues</emphasis> are all annotation
811        types. But, it is necessary to flag those annotations types meant to
812        be used as protocol parameters as such so that they
813        can identified by the Tab2Mage exporter and handled
814        appropriately.
815      </para>
816
817      <warning>
818        <para>
819          It is not possible to use the same
820          annotation type <emphasis>Temperature</emphasis> for reporting a
821          patient body temperature (which is a
822          <emphasis>Biomaterial Characteristic</emphasis>) and hybridization
823          temperature (which is a protocol parameter).
824          Hence it will be necessary to declare 2 distinct
825          annotation types:
826        </para>
827      </warning>
828     
829      <itemizedlist>
830      <listitem>
831        <para>
832        Annotation type to be used as <emphasis>BioSource
833          characteristics</emphasis>: <userinput>body temperature (degree_C)</userinput>
834        </para>
835      </listitem>
836      <listitem>
837        <para>
838        Annotation type to be used as <emphasis>protocol parameter</emphasis>:
839        <userinput>hybridization temperature (degree_C)</userinput>
840        </para>
841      </listitem>
842      </itemizedlist>
843    </sect3>
844         
845    <sect3 id="experiments_analysis.magexport.factors">
846      <title>Experimental factors</title>
847      <para>
848        It is a MIAME requirement to identify <emphasis>Experimental
849        Variables</emphasis> when submitting data to ArrayExpress
850        (provided the study is an intervention study).
851        Therefore, BASE2 users willing to use the Tab2Mage
852        export function will have to declare <emphasis>Experimental
853        Factors</emphasis> using the the <guilabel>Experimental Factor</guilabel>
854        tab available when editing experiments. See
855        <xref linkend="experiments_analysis.experiment.factors" /> for more information.
856      </para>
857     
858      <para>
859        Values for the experimental factors are take from annotations.
860        The annotation must exist at the raw bioassay level, which
861        probably means that you have to inherit the annotation from
862        some other item, for example, a biosource or a sample.
863        It is also possible to use a protocol parameter as
864        experimental factor. See <xref linkend="annotations" /> for
865        more information about annotations.
866      </para>
867    </sect3>
868  </sect2>
869</sect1>
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