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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE sect1 PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson |
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9 |
|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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12 |
|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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jari |
as published by the Free Software Foundation; either version 3 |
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peter |
of the License, or (at your option) any later version. |
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17 |
|
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BASE is distributed in the hope that it will be useful, |
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peter |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
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peter |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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peter |
GNU General Public License for more details. |
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22 |
|
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You should have received a copy of the GNU General Public License |
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jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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|
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<sect1 id="experiments_analysis.experiments"> |
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<?dbhtml filename="experiments.html" ?> |
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<title>Experiments</title> |
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<para> |
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Experiments are the starting point for analysis. When you have |
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uploaded and imported your raw data, collected and registered all |
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information and annotations about samples, bioassays, and other |
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items, it is time to collect everything in an experiment. |
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</para> |
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|
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<para> |
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To create a new experiment you can either mark one ore more |
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raw biossays on the raw bioassays list view and use the |
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<guibutton>New experiment</guibutton> button. You can also |
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create a new experiment from the experiments list view. |
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</para> |
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|
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<sect2 id="experiments_analysis.experiment.properties"> |
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<title>Experiment properties</title> |
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|
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<figure id="experiments_analysis.figures.experiment_properties"> |
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<title>Experiment properties</title> |
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<screenshot> |
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<mediaobject> |
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<imageobject><imagedata |
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fileref="figures/experiment_properties.png" format="PNG" |
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/></imageobject> |
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</mediaobject> |
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</screenshot> |
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</figure> |
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|
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|
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<helptext external_id="experiment.edit" title="Edit experiment"> |
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|
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<variablelist> |
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<varlistentry> |
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<term><guilabel>Name</guilabel></term> |
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<listitem> |
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<para> |
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The name of the experiment. |
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</para> |
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</listitem> |
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</varlistentry> |
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|
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<varlistentry> |
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<term><guilabel>Raw data type</guilabel></term> |
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<listitem> |
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<para> |
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The raw data type to use in the experiment. All raw bioassays |
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must have raw data with this type. |
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</para> |
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</listitem> |
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</varlistentry> |
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|
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<varlistentry> |
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<term><guilabel>Directory</guilabel></term> |
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<listitem> |
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<para> |
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A directory in the BASE file system where plug-ins |
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can save files that are generated during the analysis. |
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This is optional and if not given the plug-ins must ask |
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about a directory each time they need it. Use the |
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<guibutton>Select</guibutton> button to browse the file system |
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or create a new directory. |
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</para> |
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</listitem> |
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</varlistentry> |
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|
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<varlistentry> |
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<term><guilabel>Raw bioassays</guilabel></term> |
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<listitem> |
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<para> |
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The raw bioassays you want to analyze in this experiment. If |
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you created the experiment from the raw bioassays list the |
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selected raw bioassays are already filled in. Use the |
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<guibutton>Add raw bioassays</guibutton> button to add more |
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raw bioassays or the &gbRemove; button |
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to remove the selected raw bioassays from the list. |
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</para> |
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</listitem> |
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</varlistentry> |
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|
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<varlistentry> |
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<term><guilabel>Description</guilabel></term> |
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<listitem> |
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<para> |
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A description of the experiment. |
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</para> |
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</listitem> |
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</varlistentry> |
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|
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</variablelist> |
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|
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<para> |
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Click on the &gbSave; button to save the |
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changes or on &gbCancel; to abort. |
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</para> |
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|
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<seeother> |
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<other external_id="experiment.edit.publication">Publication</other> |
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<other external_id="experiment.edit.factors">Experimental factors</other> |
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</seeother> |
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</helptext> |
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|
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<sect3 id="experiments_analysis.experiment.publication"> |
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<title>The publication tab</title> |
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|
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<figure id="experiments_analysis.figures.experiment_publication"> |
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<title>Experiment publication</title> |
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<screenshot> |
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<mediaobject> |
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<imageobject><imagedata |
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fileref="figures/experiment_publication.png" format="PNG" |
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/></imageobject> |
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</mediaobject> |
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</screenshot> |
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</figure> |
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|
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<helptext external_id="experiment.edit.publication" |
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title="Experiment publication"> |
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|
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<para> |
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On this tab you can enter information about a publication |
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that is the result of the experiment. All of this information |
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is optional. |
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</para> |
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|
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<variablelist> |
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22 May 07 |
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<varlistentry> |
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<term><guilabel>PubMedId</guilabel></term> |
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<listitem> |
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<para> |
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22 May 07 |
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The ID of the publication in the |
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<ulink url="http://www.ncbi.nlm.nih.gov/pubmed/" |
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>PubMed</ulink> database. |
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</para> |
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</listitem> |
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22 May 07 |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Title</guilabel></term> |
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<listitem> |
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<para> |
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The title of the publication. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Publication date</guilabel></term> |
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<listitem> |
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<para> |
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The date the article was published. Use the |
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<guibutton>Calendar</guibutton> button to select |
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a date from a pop-up window. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term><guilabel>Abstract</guilabel></term> |
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22 May 07 |
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<listitem> |
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22 May 07 |
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<para> |
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The article abstract. |
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</para> |
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</listitem> |
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22 May 07 |
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</varlistentry> |
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22 May 07 |
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<varlistentry> |
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22 May 07 |
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<term><guilabel>Experiment design</guilabel></term> |
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22 May 07 |
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<listitem> |
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22 May 07 |
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<para> |
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An explanation of the experiment design. |
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</para> |
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</listitem> |
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22 May 07 |
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</varlistentry> |
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22 May 07 |
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<varlistentry> |
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22 May 07 |
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<term><guilabel>Experiment type</guilabel></term> |
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22 May 07 |
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<listitem> |
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22 May 07 |
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<para> |
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A description of the experiment type. |
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22 May 07 |
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</para> |
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22 May 07 |
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</listitem> |
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22 May 07 |
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</varlistentry> |
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22 May 07 |
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<varlistentry> |
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22 May 07 |
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<term><guilabel>Affiliations</guilabel></term> |
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22 May 07 |
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<listitem> |
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22 May 07 |
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<para> |
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22 May 07 |
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Partners and other related organisations that |
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have helped with the experiment. |
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</para> |
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22 May 07 |
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</listitem> |
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22 May 07 |
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</varlistentry> |
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22 May 07 |
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<varlistentry> |
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22 May 07 |
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<term><guilabel>Authors</guilabel></term> |
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22 May 07 |
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218 |
<listitem> |
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22 May 07 |
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219 |
<para> |
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22 May 07 |
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The list of authors of the publication. |
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22 May 07 |
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221 |
</para> |
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22 May 07 |
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222 |
</listitem> |
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22 May 07 |
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223 |
</varlistentry> |
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22 May 07 |
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224 |
<varlistentry> |
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22 May 07 |
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<term><guilabel>Publication</guilabel></term> |
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22 May 07 |
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226 |
<listitem> |
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22 May 07 |
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227 |
<para> |
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22 May 07 |
nicklas |
228 |
The body text of the publication. |
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22 May 07 |
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229 |
</para> |
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22 May 07 |
nicklas |
230 |
</listitem> |
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22 May 07 |
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</varlistentry> |
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22 May 07 |
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</variablelist> |
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22 May 07 |
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233 |
|
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22 May 07 |
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234 |
<para> |
3394 |
28 May 07 |
martin |
235 |
Click on the &gbSave; button to save the |
3394 |
28 May 07 |
martin |
236 |
changes or on &gbCancel; to abort. |
3362 |
22 May 07 |
nicklas |
237 |
</para> |
3362 |
22 May 07 |
nicklas |
238 |
|
3362 |
22 May 07 |
nicklas |
239 |
<seeother> |
3362 |
22 May 07 |
nicklas |
240 |
<other external_id="experiment.edit">Experiment properties</other> |
3362 |
22 May 07 |
nicklas |
241 |
<other external_id="experiment.edit.factors">Experimental factors</other> |
3362 |
22 May 07 |
nicklas |
242 |
</seeother> |
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22 May 07 |
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243 |
</helptext> |
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22 May 07 |
nicklas |
244 |
</sect3> |
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22 May 07 |
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245 |
|
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10 May 07 |
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</sect2> |
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22 May 07 |
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|
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22 May 07 |
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248 |
<sect2 id="experiments_analysis.experiment.factors"> |
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22 May 07 |
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249 |
<title>Experimental factors</title> |
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22 May 07 |
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250 |
|
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12 Oct 11 |
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<figure id="experiments_analysis.figures.experiment_factors"> |
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12 Oct 11 |
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252 |
<title>Experimental factors</title> |
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12 Oct 11 |
nicklas |
253 |
<screenshot> |
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12 Oct 11 |
nicklas |
254 |
<mediaobject> |
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<imageobject><imagedata |
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fileref="figures/experiment_factors.png" format="PNG" |
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12 Oct 11 |
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/></imageobject> |
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258 |
</mediaobject> |
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</screenshot> |
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</figure> |
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22 May 07 |
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261 |
<helptext external_id="experiment.edit.factors" |
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22 May 07 |
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262 |
title="Experimental factors"> |
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22 May 07 |
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263 |
|
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22 May 07 |
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264 |
<para> |
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22 May 07 |
nicklas |
265 |
The experimental factors of an experiment are the variables |
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22 May 07 |
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266 |
you are studying in the experiment. Typically the value of |
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22 May 07 |
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267 |
an experimental factor is varied between samples or group of samples. |
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22 May 07 |
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268 |
Different treatment methods is an example of an experimental factor. |
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22 May 07 |
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269 |
</para> |
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22 May 07 |
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270 |
|
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22 May 07 |
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<para> |
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22 May 07 |
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272 |
In the BASE world an experimental factor is the same as an annotation |
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273 |
type. Since you probably have lots of annotations on your items that are not |
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22 May 07 |
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274 |
relevant for the experiment you must select the annotations types |
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22 May 07 |
nicklas |
275 |
that should make up the experimental factors of the experiment. |
3362 |
22 May 07 |
nicklas |
276 |
</para> |
3362 |
22 May 07 |
nicklas |
277 |
|
3362 |
22 May 07 |
nicklas |
278 |
<para> |
3362 |
22 May 07 |
nicklas |
279 |
Use the <guibutton>Add annotation types</guibutton> button to |
3362 |
22 May 07 |
nicklas |
280 |
select the annotation types that should be used as experimental |
3394 |
28 May 07 |
martin |
281 |
factors. The &gbRemove; button removes the |
3362 |
22 May 07 |
nicklas |
282 |
selected annotation types. |
3362 |
22 May 07 |
nicklas |
283 |
</para> |
3362 |
22 May 07 |
nicklas |
284 |
|
3362 |
22 May 07 |
nicklas |
285 |
<para> |
3394 |
28 May 07 |
martin |
286 |
Click on the &gbSave; button to save the |
3394 |
28 May 07 |
martin |
287 |
changes or on &gbCancel; to abort. |
3362 |
22 May 07 |
nicklas |
288 |
</para> |
3362 |
22 May 07 |
nicklas |
289 |
|
3362 |
22 May 07 |
nicklas |
290 |
<para> |
3362 |
22 May 07 |
nicklas |
291 |
To be able to use the values of the experimental factors |
3362 |
22 May 07 |
nicklas |
292 |
in the analysis of your data the values must be accessible |
6961 |
01 Oct 15 |
nicklas |
293 |
from the <guilabel>root raw bioassays</guilabel>. A root raw bioassay |
6961 |
01 Oct 15 |
nicklas |
294 |
is a wrapper around a raw bioassay that is part of the experiment and |
6961 |
01 Oct 15 |
nicklas |
295 |
it has two purposes: |
3362 |
22 May 07 |
nicklas |
296 |
</para> |
3362 |
22 May 07 |
nicklas |
297 |
|
6961 |
01 Oct 15 |
nicklas |
298 |
<itemizedlist> |
6961 |
01 Oct 15 |
nicklas |
299 |
<listitem> |
6961 |
01 Oct 15 |
nicklas |
300 |
<para> |
6961 |
01 Oct 15 |
nicklas |
301 |
Hold experimental factor values for the raw bioassay in the |
6961 |
01 Oct 15 |
nicklas |
302 |
context of the current experiment without affecting other |
6961 |
01 Oct 15 |
nicklas |
303 |
experiments were the same raw bioassay is used. |
6961 |
01 Oct 15 |
nicklas |
304 |
</para> |
6961 |
01 Oct 15 |
nicklas |
305 |
</listitem> |
6961 |
01 Oct 15 |
nicklas |
306 |
<listitem> |
6961 |
01 Oct 15 |
nicklas |
307 |
<para> |
6961 |
01 Oct 15 |
nicklas |
308 |
Give the owner of the experiment control over the experimental factor |
6961 |
01 Oct 15 |
nicklas |
309 |
values used. In a multi-project setting this is important since the |
6961 |
01 Oct 15 |
nicklas |
310 |
owner of the raw bioassay may not permit changes to the raw bioassay. |
6961 |
01 Oct 15 |
nicklas |
311 |
Use the <guilabel>clone</guilabel> feature when inheriting |
6961 |
01 Oct 15 |
nicklas |
312 |
annotations to the root raw bioassay to make sure that downstream |
6961 |
01 Oct 15 |
nicklas |
313 |
analysis is not affected by changes made to the original parent |
6961 |
01 Oct 15 |
nicklas |
314 |
annotations (unless you do a manual <guilabel>resync</guilabel>). |
6961 |
01 Oct 15 |
nicklas |
315 |
</para> |
6961 |
01 Oct 15 |
nicklas |
316 |
</listitem> |
6961 |
01 Oct 15 |
nicklas |
317 |
</itemizedlist> |
6961 |
01 Oct 15 |
nicklas |
318 |
|
6961 |
01 Oct 15 |
nicklas |
319 |
<para> |
6961 |
01 Oct 15 |
nicklas |
320 |
Since most of your annotations are probably made at the sample or biosource |
6961 |
01 Oct 15 |
nicklas |
321 |
level the root raw bioassays must inherit or clone those annotations. |
6961 |
01 Oct 15 |
nicklas |
322 |
The experiment view page lists all experimental factors and their current |
6961 |
01 Oct 15 |
nicklas |
323 |
values for each root raw bioassay. |
6961 |
01 Oct 15 |
nicklas |
324 |
</para> |
6961 |
01 Oct 15 |
nicklas |
325 |
|
6961 |
01 Oct 15 |
nicklas |
326 |
<para> |
6961 |
01 Oct 15 |
nicklas |
327 |
There is a quick access to the <link linkend="annotations.batch-inherit">batch inherit</link> |
6961 |
01 Oct 15 |
nicklas |
328 |
function that makes it easy to inherit any annotations that are missing. |
6961 |
01 Oct 15 |
nicklas |
329 |
<nohelp>See also <xref linkend="annotations.inheriting" /> for more information about inheriting annotations.</nohelp> |
6961 |
01 Oct 15 |
nicklas |
330 |
</para> |
6961 |
01 Oct 15 |
nicklas |
331 |
|
6961 |
01 Oct 15 |
nicklas |
332 |
<nohelp> |
6961 |
01 Oct 15 |
nicklas |
333 |
<figure id="experiments_analysis.figures.experiment_factor_values"> |
6961 |
01 Oct 15 |
nicklas |
334 |
<title>Experimental factor values</title> |
6961 |
01 Oct 15 |
nicklas |
335 |
<screenshot> |
6961 |
01 Oct 15 |
nicklas |
336 |
<mediaobject> |
6961 |
01 Oct 15 |
nicklas |
337 |
<imageobject><imagedata |
6961 |
01 Oct 15 |
nicklas |
338 |
fileref="figures/experiment_factor_values.png" format="PNG" |
6961 |
01 Oct 15 |
nicklas |
339 |
/></imageobject> |
6961 |
01 Oct 15 |
nicklas |
340 |
</mediaobject> |
6961 |
01 Oct 15 |
nicklas |
341 |
</screenshot> |
6961 |
01 Oct 15 |
nicklas |
342 |
</figure> |
6961 |
01 Oct 15 |
nicklas |
343 |
</nohelp> |
6961 |
01 Oct 15 |
nicklas |
344 |
|
3362 |
22 May 07 |
nicklas |
345 |
<tip> |
3362 |
22 May 07 |
nicklas |
346 |
<para> |
4772 |
19 Feb 09 |
nicklas |
347 |
Use the <guilabel>Item overview</guilabel> function to |
3362 |
22 May 07 |
nicklas |
348 |
verify that all your raw bioassays has been annotated or |
3362 |
22 May 07 |
nicklas |
349 |
inherited values for all experimental factors. If not, you |
3362 |
22 May 07 |
nicklas |
350 |
should do that before starting with the analysis. |
3362 |
22 May 07 |
nicklas |
351 |
</para> |
3362 |
22 May 07 |
nicklas |
352 |
</tip> |
3362 |
22 May 07 |
nicklas |
353 |
|
3362 |
22 May 07 |
nicklas |
354 |
<seeother> |
3362 |
22 May 07 |
nicklas |
355 |
<other external_id="experiment.edit">Experiment properties</other> |
3362 |
22 May 07 |
nicklas |
356 |
<other external_id="experiment.edit.publication">Publication</other> |
4772 |
19 Feb 09 |
nicklas |
357 |
<other external_id="item.overview">Item overview</other> |
3362 |
22 May 07 |
nicklas |
358 |
<other external_id="annotations.edit.inerited">Inherit annotations</other> |
3362 |
22 May 07 |
nicklas |
359 |
</seeother> |
3362 |
22 May 07 |
nicklas |
360 |
|
3362 |
22 May 07 |
nicklas |
361 |
</helptext> |
3362 |
22 May 07 |
nicklas |
362 |
</sect2> |
3362 |
22 May 07 |
nicklas |
363 |
|
3487 |
13 Jun 07 |
peter |
364 |
</sect1> |