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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE chapter 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 Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson |
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Copyright (C) 2007 Jari Häkkinen, Nicklas Nordborg |
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|
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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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|
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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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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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|
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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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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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|
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<chapter id="array_lims" chunked="0"> |
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<title>Array LIMS</title> |
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|
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<para> |
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Arrays are at the core of the BASE business and are essential |
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elements to describe in order to |
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be <ulink url='http://www.mged.org/Workgroups/MIAME/miame.html'>MIAME</ulink> |
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compliant. It is also critical to track and manage information |
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about microarray design as accurately as possible since mistakes |
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could prove extremely costly in downstream analysis. |
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As a good practice, all array related information should be |
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entered into BASE prior to work on describing the sample |
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processing and hybridizations or other events making up an |
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experiment is begun. |
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</para> |
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|
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<sect1 id="array_lims.arraydesign"> |
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<title>Array designs</title> |
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|
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<para> |
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Array designs should be understood as a plan which can be realized during a printing |
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process producing microarray slides. During the course of the printing process, reagents |
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may run out leading to the interruption of this process. All slides created during this |
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printing process belong to the same printing batch. It is the array slide that will |
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eventually be used in a hybridization event. BASE allows user to track those 3 entities |
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with great details. This is an important functionality for users producing their own |
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arrays and for those caring for quality control and tracking of microarray slides in a |
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printing facility. The following sections detail how to use BASE to help in these |
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tasks. |
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</para> |
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|
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<note> |
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<title>Non-array platforms also need array designs</title> |
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<para> |
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Array designs are needed also for non-array platforms (eg. sequencing). In this |
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case a "virtual array design" is created which is simply a list of all features |
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that is of interest in the experiment. Since there are no coordinates or positions |
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to identify features a unique id need to be constructed in some other way. |
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For example, in sequencing experiments we may use a GTF file to create a |
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virtual array design using the <emphasis>transcript_id</emphasis> and |
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<emphasis>chromosome</emphasis> as a unique identifier. |
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</para> |
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</note> |
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|
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<para> |
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Use |
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<menuchoice> |
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<guimenu>Array LIMS</guimenu> |
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<guimenuitem>Array designs</guimenuitem> |
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</menuchoice> |
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to get to the list page with array designs. |
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</para> |
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|
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<sect2 id="array_lims.arraydesign.properties"> |
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<title>Properties</title> |
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|
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<figure id="array_lims.figures.arraydesign"> |
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<title>Array design 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/arraydesign_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="arraydesign.edit" title="Edit array design"> |
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<variablelist> |
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<varlistentry> |
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<term> |
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<guilabel>Name</guilabel> |
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</term> |
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<listitem> |
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<para>Provide an sensible name for the design (required).</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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array design. 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. |
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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>Arrays/slide</guilabel> |
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</term> |
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<listitem> |
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<para> |
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The number of sub-arrays that can be placed on a |
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single slide. The default value is 1, but some |
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platforms, for example Illumina, has slides |
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with 6 or 8 arrays. In sequencing platforms, this value |
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is the number of lanes on a flow cell. |
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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>Description</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Provide other useful information about the array design in this text |
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area. |
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</para> |
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</listitem> |
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</varlistentry> |
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</variablelist> |
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<para> |
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Click on the &gbSave; button to store the information in BASE or on the |
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&gbCancel; button to abort. |
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</para> |
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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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<para> |
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The <guilabel>Data files</guilabel> tab allows BASE users to |
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attach files to the array design. The possible file types are defined |
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by the array design's platform. See <xref linkend="platforms.selectfiles"/> |
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for more information. |
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</para> |
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|
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<para> |
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The <guilabel>Annotations</guilabel> tab allows BASE users to use |
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annotation types to refine array design description. More about annotating items |
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can be read in <xref linkend="annotations.annotating" />. |
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</para> |
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|
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<para> |
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This <guilabel>Inherited annotations</guilabel> tab contains a list of those annotations |
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that are inherited from the array design's parents (eg. plates). Information about |
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working with inherited 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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|
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<sect2 id="array_lims.arraydesign.importfeature"> |
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<title>Importing features to an array design</title> |
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|
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<para> |
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Importing features is an important step in order to fully |
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define an array design. It should be noted that BASE does not |
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enforce the immediate feature import upon creation of array |
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design. However, it is STRONGLY advised to do so when creating |
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an array design. Performing the import enables use of the |
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array design in downstream analysis with no further |
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trouble. It also matters when importing raw bioassay data and |
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matching those to the corresponding array design. |
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</para> |
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|
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<para> |
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Depending on which platform and/or data files you selected when you |
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created the array design the process to import features is different. |
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For example, if you selected the Affymetrix platform, which is a file-only |
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platform, the feature information has already been extracted from |
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the CDF file (if you selected one). If the selected platform |
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doesn't extract information from the selected data file automatically |
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this may be done manually by executing an import plug-in. |
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</para> |
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|
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<para> |
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From the array design item view, click on the &gbImport; button and use the |
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reporter map importer and an appropriate plug-in configuration when following the |
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instructions in |
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<xref linkend="import_data" />. |
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If the import run is successful, go to the array design list view. The |
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<guilabel>Has features</guilabel> |
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column will show |
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<guilabel>Yes (db: x, file: y)</guilabel> |
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where x is the number of features actually imported into the database. |
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</para> |
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|
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<note> |
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<para> |
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The &gbImport; button only shows up if the logged in user has |
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enough permissions. |
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</para> |
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</note> |
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|
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<note> |
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<title>Verify that probsets in a CDF file exist as reporters</title> |
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<para> |
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File-only platforms, such as Affymetrix, require that all probesets |
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must exist as reporters before data can be analysed. For other |
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platforms this is usually checked when importing the features to |
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the database. Since no import takes place for file-only platforms, |
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another manual step takes it place. Use the &gbImport; button |
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in the array design item view and select the |
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<guilabel>Affymetrix CDF probeset importer</guilabel> plug-in. |
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If you have enough permissions this function will also let you create |
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missing reporters. |
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</para> |
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</note> |
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</sect2> |
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</sect1> |
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|
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|
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<sect1 id="array_lims.arraybatch"> |
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<title>Array batches</title> |
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|
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<para> |
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Beside the common way of creating items in BASE, an array batch can also be created |
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directly from an array design, both in list view and single item view. |
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</para> |
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<variablelist> |
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<varlistentry> |
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<term>In list view of array design</term> |
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<listitem> |
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<para> |
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Click on the |
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<guiicon> |
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<inlinemediaobject> |
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<imageobject> |
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<imagedata fileref="figures/add.png" format="PNG" /> |
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</imageobject> |
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</inlinemediaobject> |
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</guiicon> |
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icon available from the |
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<guilabel>Batches</guilabel> |
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column of the array design you want to use. |
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<tip> |
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<para> |
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264 |
As default in BASE the |
3414 |
30 May 07 |
martin |
265 |
<guilabel>Batches</guilabel> |
3414 |
30 May 07 |
martin |
266 |
column is hidden and need therefore be made visible first, see |
3414 |
30 May 07 |
martin |
267 |
<xref linkend="webclient.itemlist.columns" /> |
3414 |
30 May 07 |
martin |
268 |
</para> |
3414 |
30 May 07 |
martin |
269 |
</tip> |
3414 |
30 May 07 |
martin |
270 |
</para> |
3370 |
23 May 07 |
philippe |
271 |
</listitem> |
3370 |
23 May 07 |
philippe |
272 |
</varlistentry> |
3414 |
30 May 07 |
martin |
273 |
</variablelist> |
3414 |
30 May 07 |
martin |
274 |
<para> |
3414 |
30 May 07 |
martin |
275 |
<guibutton>New batch…</guibutton> |
3414 |
30 May 07 |
martin |
276 |
is the corresponding button in single item view. The current array design will |
3414 |
30 May 07 |
martin |
277 |
automatically be filled in the array design property for the new batch. |
3414 |
30 May 07 |
martin |
278 |
</para> |
5796 |
10 Oct 11 |
nicklas |
279 |
|
5796 |
10 Oct 11 |
nicklas |
280 |
|
5796 |
10 Oct 11 |
nicklas |
281 |
<figure id="array_lims.figures.arraybatch"> |
5796 |
10 Oct 11 |
nicklas |
282 |
<title>Array batch properties</title> |
5796 |
10 Oct 11 |
nicklas |
283 |
<screenshot> |
5796 |
10 Oct 11 |
nicklas |
284 |
<mediaobject> |
5796 |
10 Oct 11 |
nicklas |
285 |
<imageobject> |
5796 |
10 Oct 11 |
nicklas |
286 |
<imagedata |
5796 |
10 Oct 11 |
nicklas |
287 |
fileref="figures/arraybatch_edit.png" format="PNG" /> |
5796 |
10 Oct 11 |
nicklas |
288 |
</imageobject> |
5796 |
10 Oct 11 |
nicklas |
289 |
</mediaobject> |
5796 |
10 Oct 11 |
nicklas |
290 |
</screenshot> |
5796 |
10 Oct 11 |
nicklas |
291 |
</figure> |
5796 |
10 Oct 11 |
nicklas |
292 |
|
5796 |
10 Oct 11 |
nicklas |
293 |
<helptext external_id="arraybatch.edit" |
5796 |
10 Oct 11 |
nicklas |
294 |
title="Edit array batch"> |
5796 |
10 Oct 11 |
nicklas |
295 |
|
5796 |
10 Oct 11 |
nicklas |
296 |
<variablelist> |
5796 |
10 Oct 11 |
nicklas |
297 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
298 |
<term> |
5796 |
10 Oct 11 |
nicklas |
299 |
<guilabel>Name</guilabel> |
5796 |
10 Oct 11 |
nicklas |
300 |
</term> |
5796 |
10 Oct 11 |
nicklas |
301 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
302 |
<para>The name of the array batch (required).</para> |
5796 |
10 Oct 11 |
nicklas |
303 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
304 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
305 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
306 |
<term> |
5796 |
10 Oct 11 |
nicklas |
307 |
<guilabel>Array design</guilabel> |
5796 |
10 Oct 11 |
nicklas |
308 |
</term> |
5796 |
10 Oct 11 |
nicklas |
309 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
310 |
<para>Array design that is used for the batch.</para> |
5796 |
10 Oct 11 |
nicklas |
311 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
312 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
313 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
314 |
<term> |
5796 |
10 Oct 11 |
nicklas |
315 |
<guilabel>Print robot</guilabel> |
5796 |
10 Oct 11 |
nicklas |
316 |
</term> |
5796 |
10 Oct 11 |
nicklas |
317 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
318 |
<para>The print robot that is used.</para> |
5796 |
10 Oct 11 |
nicklas |
319 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
320 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
321 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
322 |
<term> |
5796 |
10 Oct 11 |
nicklas |
323 |
<guilabel>Protocol</guilabel> |
5796 |
10 Oct 11 |
nicklas |
324 |
</term> |
5796 |
10 Oct 11 |
nicklas |
325 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
326 |
<para> |
5796 |
10 Oct 11 |
nicklas |
327 |
The printing protocol that was followed when producing the array batch |
5796 |
10 Oct 11 |
nicklas |
328 |
</para> |
5796 |
10 Oct 11 |
nicklas |
329 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
330 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
331 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
332 |
<term> |
5796 |
10 Oct 11 |
nicklas |
333 |
<guilabel>Description</guilabel> |
5796 |
10 Oct 11 |
nicklas |
334 |
</term> |
5796 |
10 Oct 11 |
nicklas |
335 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
336 |
<para> |
5796 |
10 Oct 11 |
nicklas |
337 |
Provide other useful information about the array batch in this text |
5796 |
10 Oct 11 |
nicklas |
338 |
area. |
5796 |
10 Oct 11 |
nicklas |
339 |
</para> |
5796 |
10 Oct 11 |
nicklas |
340 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
341 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
342 |
</variablelist> |
5796 |
10 Oct 11 |
nicklas |
343 |
<para> |
5796 |
10 Oct 11 |
nicklas |
344 |
Click on the &gbSave; button to store the information in BASE or on the &gbCancel; |
5796 |
10 Oct 11 |
nicklas |
345 |
button to abort. |
5796 |
10 Oct 11 |
nicklas |
346 |
</para> |
5796 |
10 Oct 11 |
nicklas |
347 |
|
5796 |
10 Oct 11 |
nicklas |
348 |
<seeother> |
5796 |
10 Oct 11 |
nicklas |
349 |
<other external_id="annotations.edit">Annotations</other> |
5796 |
10 Oct 11 |
nicklas |
350 |
<other external_id="annotations.edit.inerited">Inherit annotations</other> |
5796 |
10 Oct 11 |
nicklas |
351 |
</seeother> |
5796 |
10 Oct 11 |
nicklas |
352 |
</helptext> |
5796 |
10 Oct 11 |
nicklas |
353 |
|
3370 |
23 May 07 |
philippe |
354 |
</sect1> |
3370 |
23 May 07 |
philippe |
355 |
|
3370 |
23 May 07 |
philippe |
356 |
<sect1 id="array_lims.arrayslide"> |
3414 |
30 May 07 |
martin |
357 |
<title>Array slides</title> |
3414 |
30 May 07 |
martin |
358 |
<para> |
3414 |
30 May 07 |
martin |
359 |
Use |
3414 |
30 May 07 |
martin |
360 |
<menuchoice> |
3414 |
30 May 07 |
martin |
361 |
<guimenu>Array LIMS</guimenu> |
3414 |
30 May 07 |
martin |
362 |
<guimenuitem>Array slides</guimenuitem> |
3414 |
30 May 07 |
martin |
363 |
</menuchoice> |
3414 |
30 May 07 |
martin |
364 |
to get to the list page of array slides. |
3414 |
30 May 07 |
martin |
365 |
</para> |
3370 |
23 May 07 |
philippe |
366 |
<sect2 id="array_lims.arrayslide.create"> |
3414 |
30 May 07 |
martin |
367 |
<title>Creating array slides</title> |
4401 |
20 Aug 08 |
jari |
368 |
<para>In BASE, array slides can be created, except the common way, by 2 routes:</para> |
3414 |
30 May 07 |
martin |
369 |
<variablelist> |
3414 |
30 May 07 |
martin |
370 |
<varlistentry> |
3414 |
30 May 07 |
martin |
371 |
<term>from the array batch list page</term> |
3414 |
30 May 07 |
martin |
372 |
<listitem> |
3414 |
30 May 07 |
martin |
373 |
<para> |
3414 |
30 May 07 |
martin |
374 |
Clicking on the |
3950 |
12 Nov 07 |
martin |
375 |
<guiicon> |
3950 |
12 Nov 07 |
martin |
376 |
<inlinemediaobject> |
3950 |
12 Nov 07 |
martin |
377 |
<imageobject> |
3950 |
12 Nov 07 |
martin |
378 |
<imagedata fileref="figures/add.png" format="PNG" /> |
3950 |
12 Nov 07 |
martin |
379 |
</imageobject> |
3950 |
12 Nov 07 |
martin |
380 |
</inlinemediaobject> |
3950 |
12 Nov 07 |
martin |
381 |
</guiicon> |
3414 |
30 May 07 |
martin |
382 |
icon in the |
3414 |
30 May 07 |
martin |
383 |
<guilabel>Slides</guilabel> |
3420 |
31 May 07 |
martin |
384 |
column for the batch you want to add a slide to. Corresponding button in |
3420 |
31 May 07 |
martin |
385 |
the view page of a batch is |
3414 |
30 May 07 |
martin |
386 |
<guibutton>New slide…</guibutton> |
3414 |
30 May 07 |
martin |
387 |
. |
3414 |
30 May 07 |
martin |
388 |
</para> |
3414 |
30 May 07 |
martin |
389 |
</listitem> |
3414 |
30 May 07 |
martin |
390 |
</varlistentry> |
3414 |
30 May 07 |
martin |
391 |
<varlistentry> |
3414 |
30 May 07 |
martin |
392 |
<term>using a wizard to create multiple slides simultaneously</term> |
3414 |
30 May 07 |
martin |
393 |
<listitem> |
3414 |
30 May 07 |
martin |
394 |
<para> |
3414 |
30 May 07 |
martin |
395 |
This can be started from three different places: |
3414 |
30 May 07 |
martin |
396 |
<itemizedlist> |
3414 |
30 May 07 |
martin |
397 |
<listitem> |
3414 |
30 May 07 |
martin |
398 |
<para> |
3414 |
30 May 07 |
martin |
399 |
array batch list view by clicking on |
3950 |
12 Nov 07 |
martin |
400 |
<guiicon> |
3950 |
12 Nov 07 |
martin |
401 |
<inlinemediaobject> |
3950 |
12 Nov 07 |
martin |
402 |
<imageobject> |
5971 |
17 Feb 12 |
nicklas |
403 |
<imagedata fileref="figures/new_wizard.png" |
5971 |
17 Feb 12 |
nicklas |
404 |
format="PNG" /> |
3950 |
12 Nov 07 |
martin |
405 |
</imageobject> |
3950 |
12 Nov 07 |
martin |
406 |
</inlinemediaobject> |
3950 |
12 Nov 07 |
martin |
407 |
</guiicon> |
3414 |
30 May 07 |
martin |
408 |
in the |
3414 |
30 May 07 |
martin |
409 |
<guilabel>Slides</guilabel> |
3414 |
30 May 07 |
martin |
410 |
column of the batch that should be used. |
3414 |
30 May 07 |
martin |
411 |
</para> |
3414 |
30 May 07 |
martin |
412 |
</listitem> |
3414 |
30 May 07 |
martin |
413 |
<listitem> |
3414 |
30 May 07 |
martin |
414 |
<para> |
3414 |
30 May 07 |
martin |
415 |
Using the |
3414 |
30 May 07 |
martin |
416 |
<guibutton>Create slides</guibutton> |
3414 |
30 May 07 |
martin |
417 |
in a single item view of an array batch. |
3414 |
30 May 07 |
martin |
418 |
</para> |
3414 |
30 May 07 |
martin |
419 |
</listitem> |
3414 |
30 May 07 |
martin |
420 |
<listitem> |
3414 |
30 May 07 |
martin |
421 |
<para> |
3414 |
30 May 07 |
martin |
422 |
In the list page of array slides, using the |
3414 |
30 May 07 |
martin |
423 |
<guibutton>Create multiple…</guibutton> |
3414 |
30 May 07 |
martin |
424 |
button |
3414 |
30 May 07 |
martin |
425 |
</para> |
3414 |
30 May 07 |
martin |
426 |
</listitem> |
3414 |
30 May 07 |
martin |
427 |
</itemizedlist> |
3420 |
31 May 07 |
martin |
428 |
The wizard is described further down in |
5796 |
10 Oct 11 |
nicklas |
429 |
<xref linkend="array_lims.arrayslide.wizard" />. |
3414 |
30 May 07 |
martin |
430 |
</para> |
3414 |
30 May 07 |
martin |
431 |
</listitem> |
3414 |
30 May 07 |
martin |
432 |
</varlistentry> |
3414 |
30 May 07 |
martin |
433 |
</variablelist> |
3370 |
23 May 07 |
philippe |
434 |
|
3414 |
30 May 07 |
martin |
435 |
<figure id="write_docbook_doc.figures.arrayslide-single-create"> |
3420 |
31 May 07 |
martin |
436 |
<title>Create new array slide</title> |
3370 |
23 May 07 |
philippe |
437 |
<screenshot> |
3370 |
23 May 07 |
philippe |
438 |
<mediaobject> |
3370 |
23 May 07 |
philippe |
439 |
<imageobject> |
3423 |
31 May 07 |
nicklas |
440 |
<imagedata |
3414 |
30 May 07 |
martin |
441 |
fileref="figures/arrayslide-single-create.png" format="PNG" /> |
3370 |
23 May 07 |
philippe |
442 |
</imageobject> |
3370 |
23 May 07 |
philippe |
443 |
</mediaobject> |
3370 |
23 May 07 |
philippe |
444 |
</screenshot> |
3370 |
23 May 07 |
philippe |
445 |
</figure> |
5796 |
10 Oct 11 |
nicklas |
446 |
<helptext |
5796 |
10 Oct 11 |
nicklas |
447 |
external_id="arrayslide.edit" |
5796 |
10 Oct 11 |
nicklas |
448 |
title="Edit array slide"> |
3414 |
30 May 07 |
martin |
449 |
<variablelist> |
3414 |
30 May 07 |
martin |
450 |
<varlistentry> |
3414 |
30 May 07 |
martin |
451 |
<term> |
3414 |
30 May 07 |
martin |
452 |
<guilabel>Name</guilabel> |
3414 |
30 May 07 |
martin |
453 |
</term> |
3414 |
30 May 07 |
martin |
454 |
<listitem> |
3414 |
30 May 07 |
martin |
455 |
<para>The name of the array slide (required).</para> |
3414 |
30 May 07 |
martin |
456 |
</listitem> |
3414 |
30 May 07 |
martin |
457 |
</varlistentry> |
3414 |
30 May 07 |
martin |
458 |
<varlistentry> |
3414 |
30 May 07 |
martin |
459 |
<term> |
3414 |
30 May 07 |
martin |
460 |
<guilabel>Barcode</guilabel> |
3414 |
30 May 07 |
martin |
461 |
</term> |
3414 |
30 May 07 |
martin |
462 |
<listitem> |
3414 |
30 May 07 |
martin |
463 |
<para>Does the array slide have a barcode, it can be put here.</para> |
3414 |
30 May 07 |
martin |
464 |
</listitem> |
3414 |
30 May 07 |
martin |
465 |
</varlistentry> |
3414 |
30 May 07 |
martin |
466 |
<varlistentry> |
3414 |
30 May 07 |
martin |
467 |
<term> |
3414 |
30 May 07 |
martin |
468 |
<guilabel>Destroyed</guilabel> |
3414 |
30 May 07 |
martin |
469 |
</term> |
3414 |
30 May 07 |
martin |
470 |
<listitem> |
3414 |
30 May 07 |
martin |
471 |
<para> |
3414 |
30 May 07 |
martin |
472 |
This check-box can be ticked to mark the slide as destroyed, lost or |
3414 |
30 May 07 |
martin |
473 |
damaged. |
3414 |
30 May 07 |
martin |
474 |
</para> |
3414 |
30 May 07 |
martin |
475 |
</listitem> |
3414 |
30 May 07 |
martin |
476 |
</varlistentry> |
3414 |
30 May 07 |
martin |
477 |
<varlistentry> |
3414 |
30 May 07 |
martin |
478 |
<term> |
3414 |
30 May 07 |
martin |
479 |
<guilabel>Array batch</guilabel> |
3414 |
30 May 07 |
martin |
480 |
</term> |
3414 |
30 May 07 |
martin |
481 |
<listitem> |
3414 |
30 May 07 |
martin |
482 |
<para>Array batch that the slide belongs to (required).</para> |
3414 |
30 May 07 |
martin |
483 |
</listitem> |
3414 |
30 May 07 |
martin |
484 |
</varlistentry> |
3414 |
30 May 07 |
martin |
485 |
<varlistentry> |
3414 |
30 May 07 |
martin |
486 |
<term> |
3414 |
30 May 07 |
martin |
487 |
<guilabel>Index</guilabel> |
3414 |
30 May 07 |
martin |
488 |
</term> |
3414 |
30 May 07 |
martin |
489 |
<listitem> |
3420 |
31 May 07 |
martin |
490 |
<para>The index of the array slide in selected array batch.</para> |
3414 |
30 May 07 |
martin |
491 |
</listitem> |
3414 |
30 May 07 |
martin |
492 |
</varlistentry> |
3414 |
30 May 07 |
martin |
493 |
<varlistentry> |
3414 |
30 May 07 |
martin |
494 |
<term> |
3414 |
30 May 07 |
martin |
495 |
<guilabel>Description</guilabel> |
3414 |
30 May 07 |
martin |
496 |
</term> |
3414 |
30 May 07 |
martin |
497 |
<listitem> |
3414 |
30 May 07 |
martin |
498 |
<para> |
3414 |
30 May 07 |
martin |
499 |
Any information useful information about the slide can be in this field. |
3414 |
30 May 07 |
martin |
500 |
</para> |
3414 |
30 May 07 |
martin |
501 |
</listitem> |
3414 |
30 May 07 |
martin |
502 |
</varlistentry> |
3414 |
30 May 07 |
martin |
503 |
</variablelist> |
3414 |
30 May 07 |
martin |
504 |
<para> |
4401 |
20 Aug 08 |
jari |
505 |
Click on the &gbSave; button to store the information in BASE or on the &gbCancel; |
3414 |
30 May 07 |
martin |
506 |
button to abort. |
3414 |
30 May 07 |
martin |
507 |
</para> |
5796 |
10 Oct 11 |
nicklas |
508 |
<seeother> |
5796 |
10 Oct 11 |
nicklas |
509 |
<other external_id="arrayslide.createwizard.1">Create array slides - step 1</other> |
5796 |
10 Oct 11 |
nicklas |
510 |
<other external_id="arrayslide.createwizard.2">Create array slides - step 2</other> |
5796 |
10 Oct 11 |
nicklas |
511 |
</seeother> |
5796 |
10 Oct 11 |
nicklas |
512 |
</helptext> |
5796 |
10 Oct 11 |
nicklas |
513 |
</sect2> |
5796 |
10 Oct 11 |
nicklas |
514 |
|
5796 |
10 Oct 11 |
nicklas |
515 |
<sect2 id="array_lims.arrayslide.wizard"> |
3414 |
30 May 07 |
martin |
516 |
<title>Multiple slides wizard</title> |
3414 |
30 May 07 |
martin |
517 |
<para> |
3414 |
30 May 07 |
martin |
518 |
As mentioned above there is an alternative to create one slide at a time if you |
3420 |
31 May 07 |
martin |
519 |
have many to add. There is a wizard that can help you to create at the most 999 |
5796 |
10 Oct 11 |
nicklas |
520 |
slides in one go. The wizard is in two steps: |
5796 |
10 Oct 11 |
nicklas |
521 |
</para> |
5796 |
10 Oct 11 |
nicklas |
522 |
|
5796 |
10 Oct 11 |
nicklas |
523 |
<figure id="array_lims.figures.arrayslide-wizard-step1"> |
5796 |
10 Oct 11 |
nicklas |
524 |
<title>Create multiple array slides - step 1</title> |
5796 |
10 Oct 11 |
nicklas |
525 |
<screenshot> |
5796 |
10 Oct 11 |
nicklas |
526 |
<mediaobject> |
5796 |
10 Oct 11 |
nicklas |
527 |
<imageobject> |
5796 |
10 Oct 11 |
nicklas |
528 |
<imagedata fileref="figures/arrayslide-wizard-step1.png" format="PNG" /> |
5796 |
10 Oct 11 |
nicklas |
529 |
</imageobject> |
5796 |
10 Oct 11 |
nicklas |
530 |
</mediaobject> |
5796 |
10 Oct 11 |
nicklas |
531 |
</screenshot> |
5796 |
10 Oct 11 |
nicklas |
532 |
</figure> |
5796 |
10 Oct 11 |
nicklas |
533 |
|
5796 |
10 Oct 11 |
nicklas |
534 |
<helptext external_id="arrayslide.createwizard.1" |
5796 |
10 Oct 11 |
nicklas |
535 |
title="Create array slides - step 1"> |
5796 |
10 Oct 11 |
nicklas |
536 |
|
5796 |
10 Oct 11 |
nicklas |
537 |
<para> |
5796 |
10 Oct 11 |
nicklas |
538 |
The first step reminds alot of the normal edit window of an array |
5796 |
10 Oct 11 |
nicklas |
539 |
slide: |
5796 |
10 Oct 11 |
nicklas |
540 |
</para> |
5796 |
10 Oct 11 |
nicklas |
541 |
|
5796 |
10 Oct 11 |
nicklas |
542 |
<variablelist> |
5796 |
10 Oct 11 |
nicklas |
543 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
544 |
<term> |
5796 |
10 Oct 11 |
nicklas |
545 |
<guilabel>Name</guilabel> |
5796 |
10 Oct 11 |
nicklas |
546 |
</term> |
5796 |
10 Oct 11 |
nicklas |
547 |
<listitem> |
3414 |
30 May 07 |
martin |
548 |
<para> |
5796 |
10 Oct 11 |
nicklas |
549 |
The name prefix of the array slides. Each array slide will be |
5796 |
10 Oct 11 |
nicklas |
550 |
numbered according to the <emphasis>start at</emphasis> and |
5796 |
10 Oct 11 |
nicklas |
551 |
<emphasis>pad size</emphasis> settings below. |
3414 |
30 May 07 |
martin |
552 |
</para> |
5796 |
10 Oct 11 |
nicklas |
553 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
554 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
555 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
556 |
<term> |
5796 |
10 Oct 11 |
nicklas |
557 |
<guilabel>Array batch</guilabel> |
5796 |
10 Oct 11 |
nicklas |
558 |
</term> |
5796 |
10 Oct 11 |
nicklas |
559 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
560 |
<para>Array batch that the slides belongs to (required).</para> |
5796 |
10 Oct 11 |
nicklas |
561 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
562 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
563 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
564 |
<term> |
5796 |
10 Oct 11 |
nicklas |
565 |
<guilabel>Quantity</guilabel> |
5796 |
10 Oct 11 |
nicklas |
566 |
</term> |
5796 |
10 Oct 11 |
nicklas |
567 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
568 |
<para> |
5796 |
10 Oct 11 |
nicklas |
569 |
Number of slides to create with this wizard |
5796 |
10 Oct 11 |
nicklas |
570 |
(required and must be between 1 and 999) |
5796 |
10 Oct 11 |
nicklas |
571 |
</para> |
5796 |
10 Oct 11 |
nicklas |
572 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
573 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
574 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
575 |
<term> |
5796 |
10 Oct 11 |
nicklas |
576 |
<guilabel>Start at</guilabel> |
5796 |
10 Oct 11 |
nicklas |
577 |
</term> |
5796 |
10 Oct 11 |
nicklas |
578 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
579 |
<para> |
5796 |
10 Oct 11 |
nicklas |
580 |
The index number to start from when indexing the |
5796 |
10 Oct 11 |
nicklas |
581 |
name of the slides. |
5796 |
10 Oct 11 |
nicklas |
582 |
</para> |
5796 |
10 Oct 11 |
nicklas |
583 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
584 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
585 |
<varlistentry> |
5796 |
10 Oct 11 |
nicklas |
586 |
<term> |
5796 |
10 Oct 11 |
nicklas |
587 |
<guilabel>Pad size</guilabel> |
5796 |
10 Oct 11 |
nicklas |
588 |
</term> |
5796 |
10 Oct 11 |
nicklas |
589 |
<listitem> |
5796 |
10 Oct 11 |
nicklas |
590 |
<para> |
5796 |
10 Oct 11 |
nicklas |
591 |
The index will be filled out with zeros in front to |
5796 |
10 Oct 11 |
nicklas |
592 |
always have this length. |
5796 |
10 Oct 11 |
nicklas |
593 |
</para> |
5796 |
10 Oct 11 |
nicklas |
594 |
</listitem> |
5796 |
10 Oct 11 |
nicklas |
595 |
</varlistentry> |
5796 |
10 Oct 11 |
nicklas |
596 |
</variablelist> |
5796 |
10 Oct 11 |
nicklas |
597 |
|
5796 |
10 Oct 11 |
nicklas |
598 |
<para> |
5796 |
10 Oct 11 |
nicklas |
599 |
Click on &gbNext; to move on to the second step of the wizard. |
5796 |
10 Oct 11 |
nicklas |
600 |
</para> |
5796 |
10 Oct 11 |
nicklas |
601 |
|
5796 |
10 Oct 11 |
nicklas |
602 |
<seeother> |
5796 |
10 Oct 11 |
nicklas |
603 |
<other external_id="arrayslide.createwizard.2">Create array slides - step 2</other> |
5796 |
10 Oct 11 |
nicklas |
604 |
<other external_id="arrayslide.edit">Edit array slide</other> |
5796 |
10 Oct 11 |
nicklas |
605 |
</seeother> |
5796 |
10 Oct 11 |
nicklas |
606 |
|
5796 |
10 Oct 11 |
nicklas |
607 |
</helptext> |
5796 |
10 Oct 11 |
nicklas |
608 |
|
5796 |
10 Oct 11 |
nicklas |
609 |
|
5796 |
10 Oct 11 |
nicklas |
610 |
<figure id="array_lims.figures.arrayslide-wizard-step2"> |
5796 |
10 Oct 11 |
nicklas |
611 |
<title>Create multiple array slides - step 2</title> |
3420 |
31 May 07 |
martin |
612 |
<screenshot> |
3420 |
31 May 07 |
martin |
613 |
<mediaobject> |
3420 |
31 May 07 |
martin |
614 |
<imageobject> |
5796 |
10 Oct 11 |
nicklas |
615 |
<imagedata fileref="figures/arrayslide-wizard-step2.png" format="PNG" /> |
3420 |
31 May 07 |
martin |
616 |
</imageobject> |
3420 |
31 May 07 |
martin |
617 |
</mediaobject> |
3420 |
31 May 07 |
martin |
618 |
</screenshot> |
3420 |
31 May 07 |
martin |
619 |
</figure> |
5796 |
10 Oct 11 |
nicklas |
620 |
|
5796 |
10 Oct 11 |
nicklas |
621 |
<helptext external_id="arrayslide.createwizard.2" title="Create array slides - step 2"> |
5796 |
10 Oct 11 |
nicklas |
622 |
<para> |
5796 |
10 Oct 11 |
nicklas |
623 |
This step allows the names of the array slides to be adjusted |
5796 |
10 Oct 11 |
nicklas |
624 |
if needed. It is also possible to enter barcodes for each of the |
5796 |
10 Oct 11 |
nicklas |
625 |
new slides. The information can either be filled in one-by-one |
5796 |
10 Oct 11 |
nicklas |
626 |
or by using the "scratchpad" icon |
5796 |
10 Oct 11 |
nicklas |
627 |
<guiicon> |
5796 |
10 Oct 11 |
nicklas |
628 |
<inlinemediaobject> |
5796 |
10 Oct 11 |
nicklas |
629 |
<imageobject> |
5796 |
10 Oct 11 |
nicklas |
630 |
<imagedata fileref="figures/paste.png" |
5796 |
10 Oct 11 |
nicklas |
631 |
format="PNG" /> |
5796 |
10 Oct 11 |
nicklas |
632 |
</imageobject> |
5796 |
10 Oct 11 |
nicklas |
633 |
</inlinemediaobject> |
5796 |
10 Oct 11 |
nicklas |
634 |
</guiicon>. This opens up a larger text window where the names or barcodes |
5796 |
10 Oct 11 |
nicklas |
635 |
can be entered one per line. This can be useful if the information can be |
5796 |
10 Oct 11 |
nicklas |
636 |
pasted from an external source. |
5796 |
10 Oct 11 |
nicklas |
637 |
</para> |
5796 |
10 Oct 11 |
nicklas |
638 |
|
5796 |
10 Oct 11 |
nicklas |
639 |
<seeother> |
5796 |
10 Oct 11 |
nicklas |
640 |
<other external_id="arrayslide.createwizard.1">Create array slides - step 1</other> |
5796 |
10 Oct 11 |
nicklas |
641 |
<other external_id="arrayslide.edit">Edit array slide</other> |
5796 |
10 Oct 11 |
nicklas |
642 |
</seeother> |
5796 |
10 Oct 11 |
nicklas |
643 |
|
5796 |
10 Oct 11 |
nicklas |
644 |
<para> |
5796 |
10 Oct 11 |
nicklas |
645 |
Click on the &gbSave; button to store the information in BASE or on the |
5796 |
10 Oct 11 |
nicklas |
646 |
&gbCancel; button to abort the wizard. |
5796 |
10 Oct 11 |
nicklas |
647 |
</para> |
5796 |
10 Oct 11 |
nicklas |
648 |
|
5796 |
10 Oct 11 |
nicklas |
649 |
</helptext> |
5796 |
10 Oct 11 |
nicklas |
650 |
|
3370 |
23 May 07 |
philippe |
651 |
</sect2> |
3370 |
23 May 07 |
philippe |
652 |
</sect1> |
3370 |
23 May 07 |
philippe |
653 |
</chapter> |