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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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7 |
|
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Copyright (C) 2007 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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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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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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13 Jun 07 |
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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11 Sep 08 |
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.rawbioassay"> |
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<?dbhtml filename="rawbioassays.html" ?> |
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<title>Raw bioassays</title> |
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<para> |
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A <guilabel>Raw bioassay</guilabel> is the representation |
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of the result of analyzing data from the physical bioassay |
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down to the point where we have a file or a set of files |
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containing measurements per feature (eg. spot, gene, etc.) |
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for a single sample or extract. Further analysis is usually |
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needed before we can say something about individual features |
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or samples and how they relate to each other. This |
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kind of analisys is done in <guilabel>Experiments</guilabel>. |
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See <xref linkend="experiments_analysis.experiments" />. |
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</para> |
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|
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<para> |
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The term <guilabel>Raw bioassay</guilabel> is bit misleading since the |
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real "raw data" is actually the images from a microarray scan or the |
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output from a sequencer. For historical reasons we have chosen to keep |
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the term raw bioassay since this represents the first possibility for |
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a transition between file-base data and database-stored data. Typically, |
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all pre-rawbioassay analysis is done outside of BASE, and although |
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we now have the possibility to track this in detail, it will |
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probably remain so for some time in the future. See |
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<xref linkend="experiments_analysis.derivedbioassays" />. |
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|
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</para> |
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|
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<sect2 id="experiments_analysis.rawbioassay.create"> |
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<title>Create raw bioassays</title> |
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<para> |
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Creating a new raw bioassay is a two- or three-step process: |
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</para> |
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|
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<orderedlist> |
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<listitem> |
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<para> |
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Create a new raw bioassay item with the &gbNew; button in the raw bioassays list view. |
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It is also possible to create raw bioassays from the derived bioassays |
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list- and single view- page. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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Upload the file(s) with the raw data and attach them to the |
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raw bioassay. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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The used platform may require that data is imported to the database. |
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See <xref linkend="import_data" />. If the platform is a |
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file-only platform, this step can be skipped. |
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</para> |
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</listitem> |
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</orderedlist> |
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|
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<note> |
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<title>Supported file formats</title> |
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BASE has built-in support for most file formats where the data comes |
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in a tab-separated (or similar) form. Data for one raw bioassay |
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must be in a single file. Support for other file formats |
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may be added through plug-ins. |
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</note> |
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</sect2> |
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|
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<sect2 id="experiments_analysis.rawbioassay.properties"> |
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<title>Raw bioassay properties</title> |
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|
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<figure |
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id="experiments_analysis.figures.rawbioassay.edit"> |
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<title>Raw bioassay properties</title> |
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<screenshot> |
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<mediaobject> |
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<imageobject> |
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<imagedata |
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fileref="figures/rawbioassay_edit.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="rawbioassay.edit" title="Edit raw bioassay"> |
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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 raw bioassay. |
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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> |
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<guilabel>Platform</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Select the platform / variant used for the |
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raw bioassay. The selected options affects which |
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files that can be selected on the <guilabel>Data files</guilabel> |
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tab. If the platform supports importing data to the database |
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you must also select a <guilabel>Raw data type</guilabel>. |
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</para> |
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nicklas |
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</listitem> |
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</varlistentry> |
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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 type of raw data. This option is disabled for file-only |
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nicklas |
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platforms and for platforms that are locked to a specific |
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raw data type. This cannot be changed after raw data has been |
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imported. <nohelp>See |
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<xref linkend="experiments_analysis.rawdatatypes" />.</nohelp> |
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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>Parent bioassay</guilabel></term> |
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nicklas |
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<listitem> |
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nicklas |
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<para> |
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nicklas |
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The derived bioassay that is the parent of this |
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raw bioassay. |
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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>Parent extract</guilabel></term> |
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05 Oct 11 |
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<listitem> |
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05 Oct 11 |
nicklas |
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<para> |
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05 Oct 11 |
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The extract which this raw bioassay has measured. This is normally selected |
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among the extracts that are linked with the physical bioassay that this |
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nicklas |
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raw bioassay is coming from. Selecting the correct extract is important if the |
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physical bioassay contains more than one extract, since otherwise it may affect |
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nicklas |
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how annotations are inherited and used in downstream analysis. |
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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>Array design</guilabel></term> |
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<listitem> |
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<para> |
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The array design used on the array slide (optional). |
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nicklas |
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If an array design is specified |
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the import will verify that the raw data has |
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nicklas |
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the same reporter on the same position. This |
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prevents mistakes but also speed up analysis |
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since some optimizations can be used when assigning |
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positions in bioassay sets. |
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The array design can be changed after raw data has been |
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imported, but this triggers a new validation. If the raw data |
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enell |
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is stored in the database, the features on the new array design must |
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enell |
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match the the raw data. The verification can use three different methods: |
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enell |
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</para> |
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enell |
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|
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<itemizedlist> |
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<listitem> |
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<para> |
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Coordinates: Verify block, meta-grid, row and column coordinates. |
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</para> |
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</listitem> |
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<listitem> |
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<para>Position: Verify the position number.</para> |
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enell |
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</listitem> |
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<listitem> |
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<para> |
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Feature ID: Verify the feature ID. This option can only be used |
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enell |
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if the raw bioassay is currently connected to an array design that |
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enell |
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has feature ID values already. |
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</para> |
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</listitem> |
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</itemizedlist> |
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<para> |
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In all three cases it is also verified that the reporter of the raw |
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data matches the reporter of the features. |
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</para> |
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|
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<para> |
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enell |
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For Affymetrix data, the |
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nicklas |
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CEL file is validated against the CDF file of the new array design. |
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If the validation fails, the array design is not changed. |
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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>Software</guilabel></term> |
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<listitem> |
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<para> |
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The software used to generate the raw data (optional). |
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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>Protocol</guilabel></term> |
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<listitem> |
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<para> |
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The protocol used when generating the raw data (optional). |
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Software parameters may be registered as part of |
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the protocol. |
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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>Description</guilabel></term> |
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<listitem> |
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<para> |
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A description of the raw bioassay (optional). |
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</para> |
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</listitem> |
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</varlistentry> |
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</variablelist> |
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|
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<seeother> |
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<other external_id="datafiles.edit">Data files</other> |
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<other external_id="annotations.edit">Annotations</other> |
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<other external_id="annotations.edit.inerited">Inherit annotations</other> |
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</seeother> |
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</helptext> |
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|
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|
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<para> |
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The <guilabel>Data files</guilabel> tab allows BASE users to select |
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nicklas |
251 |
files that contains data for the raw bioassay. |
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12 Oct 11 |
nicklas |
252 |
Read more about this in <xref linkend="platforms.selectfiles" />. |
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nicklas |
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</para> |
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12 Oct 11 |
nicklas |
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|
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<para> |
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12 Oct 11 |
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The <guilabel>Annotations</guilabel> tab allows BASE users to use |
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12 Oct 11 |
nicklas |
257 |
annotation types to refine bioassay description. More about annotating items |
5800 |
12 Oct 11 |
nicklas |
258 |
can be read in <xref linkend="annotations.annotating" /> |
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12 Oct 11 |
nicklas |
259 |
</para> |
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10 May 07 |
nicklas |
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|
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<para> |
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12 Oct 11 |
nicklas |
262 |
This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations |
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12 Oct 11 |
nicklas |
263 |
that are inherited from the bioassay's parents. Information about working with inherited |
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12 Oct 11 |
nicklas |
264 |
annotations can be found in <xref linkend="annotations.inheriting" />. |
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</para> |
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|
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</sect2> |
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|
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<sect2 id="experiments_analysis.rawbioassay.rawdata"> |
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<title>Import raw data</title> |
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<para> |
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Depending on the platform, raw data may have to be imported after |
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nicklas |
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you have created the raw bioassay item. This section doesn't apply |
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nicklas |
274 |
to file-only platforms. The import is handled by plug-ins. To start |
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10 May 07 |
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the import click on the <guibutton>Import…</guibutton> |
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button on the single-item view for the raw bioassay. |
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peter |
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If this button does not appear it may be because no file |
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format has been specified for the raw data type used by the |
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13 Jun 07 |
peter |
279 |
raw bioassay or that the logged in user does not have permission |
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to use the import plug-in or file format. |
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jari |
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See <xref linkend="import_data" /> for more |
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information. |
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</para> |
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|
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<note> |
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<title>File-only platforms</title> |
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File-only platforms, such as Affymetrix, is handled differently and data is not |
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nicklas |
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imported into the database. |
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</note> |
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|
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</sect2> |
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|
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13 Jun 07 |
peter |
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<sect2 id="experiments_analysis.rawdatatypes"> |
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13 Jun 07 |
peter |
294 |
<title>Raw data types</title> |
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13 Jun 07 |
peter |
295 |
|
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nicklas |
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<para> |
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23 Oct 07 |
nicklas |
297 |
A raw data type defines the types of measured values that can be stored |
5783 |
05 Oct 11 |
nicklas |
298 |
for individual features in the database. Usually this includes some |
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23 Oct 07 |
nicklas |
299 |
kind of foreground and background intensity values. The number and meaning |
5783 |
05 Oct 11 |
nicklas |
300 |
of the values usually depends on the hardware and software used to analyze |
5783 |
05 Oct 11 |
nicklas |
301 |
the data from the experiment. Many tools provide mean and median values, |
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23 Oct 07 |
nicklas |
302 |
standard deviations, quality control information, etc. Since there are so |
3872 |
23 Oct 07 |
nicklas |
303 |
many existing tools with many different data file formats BASE uses a |
3872 |
23 Oct 07 |
nicklas |
304 |
separate database table for each raw data type to store data. The raw data |
3872 |
23 Oct 07 |
nicklas |
305 |
tables have been optimized for the type of raw data they can hold and only |
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23 Oct 07 |
nicklas |
306 |
has the columns that are needed to store the data. BASE ships with a large |
3872 |
23 Oct 07 |
nicklas |
307 |
number of pre-defined raw data types. An administrator may also define |
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23 Oct 07 |
nicklas |
308 |
additional raw data type. See <xref linkend="appendix.rawdatatypes" /> |
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23 Oct 07 |
nicklas |
309 |
for more information. |
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23 Oct 07 |
nicklas |
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</para> |
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23 Oct 07 |
nicklas |
311 |
|
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23 Oct 07 |
nicklas |
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<sect3 id="experiments_analysis.fileonly"> |
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23 Oct 07 |
nicklas |
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<title>File-only platforms</title> |
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23 Oct 07 |
nicklas |
314 |
<para> |
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05 Oct 11 |
nicklas |
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In some cases it doesn't make sense to import any data into the |
5783 |
05 Oct 11 |
nicklas |
316 |
database. The main reason is that performance will suffer as the |
5783 |
05 Oct 11 |
nicklas |
317 |
number of entries in the database gets higher. A typical Genepix file |
5783 |
05 Oct 11 |
nicklas |
318 |
contains ~55K spots while an Affymetrix file may have millions. |
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23 Oct 07 |
nicklas |
319 |
</para> |
3872 |
23 Oct 07 |
nicklas |
320 |
<para> |
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23 Oct 07 |
nicklas |
321 |
The drawback of keeping the data in files is that none of the generic |
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23 Oct 07 |
nicklas |
322 |
tools in BASE can read it. Special plug-ins must be developed for each |
3872 |
23 Oct 07 |
nicklas |
323 |
type of data file that can be used to analyze and visualize the data. |
3872 |
23 Oct 07 |
nicklas |
324 |
For the Affymetrix platform there are implementations of the RMAExpress |
3872 |
23 Oct 07 |
nicklas |
325 |
and Plier normalizations available on the BASE plug-ins web site. |
3872 |
23 Oct 07 |
nicklas |
326 |
BASE also ships with built-in plug-ins for extracting metadata from |
3872 |
23 Oct 07 |
nicklas |
327 |
Affymetrix CEL and CDF files (ie. headers, number of spots, etc). |
3872 |
23 Oct 07 |
nicklas |
328 |
</para> |
3872 |
23 Oct 07 |
nicklas |
329 |
<para> |
3872 |
23 Oct 07 |
nicklas |
330 |
Users of other file-only platforms should check the BASE plug-ins |
3872 |
23 Oct 07 |
nicklas |
331 |
website for plug-ins related to their platform. If they can't |
3872 |
23 Oct 07 |
nicklas |
332 |
find any we recommend that they try to find other users of the same |
3872 |
23 Oct 07 |
nicklas |
333 |
platform and try to cooperate in developing the required tools and |
3872 |
23 Oct 07 |
nicklas |
334 |
plug-ins. |
3872 |
23 Oct 07 |
nicklas |
335 |
</para> |
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13 Jun 07 |
peter |
336 |
</sect3> |
3487 |
13 Jun 07 |
peter |
337 |
|
3487 |
13 Jun 07 |
peter |
338 |
</sect2> |
3487 |
13 Jun 07 |
peter |
339 |
|
3487 |
13 Jun 07 |
peter |
340 |
</sect1> |
3487 |
13 Jun 07 |
peter |
341 |
|