Changeset 3370


Ignore:
Timestamp:
May 23, 2007, 7:31:47 PM (14 years ago)
Author:
philippe
Message:
 
File:
1 edited

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  • trunk/doc/src/docbook/userdoc/array_lims.xml

    r3246 r3370  
    3030  <?dbhtml dir="array_lims"?>
    3131  <title>Array LIMS</title>
    32     <sect1>
    33       <title></title>
    34       <para></para>
    35     </sect1>
     32  <sect1>
     33    <title>Introduction</title>
     34
     35    <para>Arrays are at the core of the BASE2 business and are essential elements to describe in
     36      order to be MIAME compliant. It is also critical to track and manage information about
     37      microarray design as accurately as possible since mistakes could prove extremely costly
     38      in downstream analysis.</para>
     39    <para>Finally, as a good practice, all Array related information should be entered into
     40      BASE2 system prior to start describing the sample processing and hybridizations events
     41      making up a microarray experiment.</para>
     42
     43    <para>BASE2 has been engineered to support microarray printing facilities. The system
     44      therefore offers objects to describe plates, their geometries and the events (merging,
     45      printing) affected them. The first section of the chapter deals with this functionality.
     46      as well as plate management.</para>
     47
     48    <para>For users buying their arrays from commercial sources, the Plate Management component
     49      can be ignored and they can go immediatly to the second section <xref
     50        linkend="array_lims.arraydesign"/> of the chapter.</para>
     51
     52  </sect1>
     53
     54  <sect1 id="array_lims.platemanagement">
     55    <title>Managing Plates</title>
     56    <para>TO DO</para>
     57  </sect1>
     58
     59  <sect1 id="array_lims.arraydesign">
     60    <title>Managing ArrayDesigns</title>
     61    <para> ArrayDesign should be understood as a plan which can be realized during a printing
     62      process producing microarray slides. During the course of the printing process, reagents
     63      may run out leading to the interruption of this process. All slides created during this
     64      printing process belong to the same printing 'batch'. It is the array slide that will
     65      eventually be used in a Hybridization event. BASE2 allows user to track those 3 entities
     66      with great details. This is an important functionality for users producing their own
     67      arrays and for those caring for quality control and tracking of microarray slides in a
     68      printing facility. The following sections detail how to use BASE2 to help in these
     69      tasks. </para>
     70    <sect2 id="array_lims.arraydesign.create">
     71      <title>Creating ArrayDesigns</title>
     72      <para>To create an ArrayDesign, do the following</para>
     73      <para>Go To <menuchoice>
     74          <guimenu>Array LIMS</guimenu>
     75          <guimenuitem>ArrayDesign</guimenuitem>
     76        </menuchoice>
     77      </para>
     78      <para>The ArrayDesign List view now presents all ArrayDesigns available to the user
     79        (shared to or owned by).</para>
     80      <para>Click on <guibutton>New&hellip;</guibutton> button</para>
     81      <para>A 'Create' pop-up window opens. It contains 3 tabs</para>
     82
     83      <variablelist>
     84        <varlistentry>
     85          <term>
     86            <guilabel>Array design</guilabel>
     87          </term>
     88          <listitem>
     89
     90            <para>The tab contains four fields, namely:</para>
     91
     92            <variablelist>
     93
     94              <varlistentry>
     95                <term>
     96                  <guilabel>Name</guilabel>
     97                </term>
     98                <listitem>
     99                  <para> Provide a unique sensible name for the design. Possibly
     100                    follow the convention [organisation-species-feature
     101                    number-version] as in EMBL-Hsapiens-wholegenome-45k-v1. For
     102                    commercial platforms such as Agilent and Affymetrix, it is
     103                    probably better to use the commercial names, such as Agilent
     104                    Whole Mouse Genome G4122A or HG_U133A respectively</para>
     105                </listitem>
     106              </varlistentry>
     107
     108              <varlistentry>
     109                <term>
     110                  <guilabel>Description</guilabel>
     111                </term>
     112                <listitem>
     113                  <para>Provide a short but meaningful of the ArrayDesign</para>
     114                </listitem>
     115              </varlistentry>
     116
     117              <varlistentry>
     118                <term>
     119                  <guilabel>Affy Chip</guilabel>
     120                </term>
     121                <listitem>
     122                  <para>This is a radio button for providing a boolean entry,
     123                    essentially telling the system whether the ArrayDesign being
     124                    created is of Affymetrix technology or not.</para>
     125                  <warning>
     126                    <para>As indicated on the interface, once saved, this
     127                      information cannot be modified, so if a mistake is made,
     128                      the entry will have to be deleted.</para>
     129                  </warning>
     130                </listitem>
     131              </varlistentry>
     132
     133              <varlistentry>
     134                <term>
     135                  <guilabel>CDF file</guilabel>
     136                </term>
     137                <listitem>
     138                  <para>This field allows to upload an Affymetrix CDF file. A CDF
     139                    file is a binary file describing Affymetrix chip layout.
     140                    This file is necessary for performing analysis using BASE2
     141                    plugins (e.g RMAExpress plugin).</para>
     142                  <note>
     143                    <para>Affymetrix users, you can also upload CLF or BPMAP
     144                      files defined for exon and tiling arrays
     145                    respectively.</para>
     146                  </note>
     147                </listitem>
     148              </varlistentry>
     149
     150            </variablelist>
     151          </listitem>
     152        </varlistentry>
     153
     154        <varlistentry>
     155          <term>
     156            <guilabel>Annotations</guilabel>
     157          </term>
     158          <listitem>
     159            <para>This tab allows to input values associated to Annotation Types devised
     160              to refine ArrayDesign description.</para>
     161            <para>The windows will be empty if no Annotation Types have been declared to
     162              annotation ArrayDesign item or if none are shared to the user</para>
     163          </listitem>
     164        </varlistentry>
     165
     166        <varlistentry>
     167          <term>
     168            <guilabel>Inherited Annotations</guilabel>
     169          </term>
     170          <listitem>
     171            <para>TO DO</para>
     172          </listitem>
     173        </varlistentry>
     174
     175      </variablelist>
     176      <para>Click on the <inlinemediaobject>
     177          <imageobject>
     178            <imagedata fileref="figures/save.gif" format="GIF"/>
     179          </imageobject>
     180        </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
     181          <imageobject>
     182            <imagedata fileref="figures/cancel.gif" format="GIF"/>
     183          </imageobject>
     184        </inlinemediaobject> button to abort. </para>
     185      <para>Upon saving, the Array Design List View page is displayed. Users should pay
     186        attention to the column <guilabel>Has features</guilabel>. Unless an Affymetrix
     187        ArrayDesign was created, the value will be by default set to
     188        <guilabel>no</guilabel>. For all other cases, this value will only be updated
     189        following <guilabel>Importing the Features</guilabel>, a process which is detailed
     190        in the next section.</para>
     191
     192    </sect2>
     193
     194    <sect2 id="array_lims.arraydesign.importfeature">
     195      <title>Importing Features associated to an ArrayDesign</title>
     196      <important>
     197        <para>For non-Affymetrix ArrayDesigns, Importing Features is an important step in
     198          order to fully define an ArrayDesign. It should be noted that BASE2 does not
     199          enforce the immediate Feature import upon creation of ArrayDesign. However, It
     200          is STRONGLY advised to do so when creating an ArrayDesign. Doing so enables to
     201          use the Array Design for downstream analysis with no further trouble. It also
     202          matters when importing rawBioassay data and matching those to the corresponding
     203          ArrayDesign. It is interesting to note that the processes of importing features
     204          associated to Array Design and importing Data associated to Raw BioAssay are in
     205          essence very similar.</para> Please see section <xref
     206          linkend="experiments_analysis.rawbioassay.rawdata"/> for more information. </important>
     207      <para>This section applies only to non-affymetrix ArrayDesign since Affymetrix designs
     208        are handled differently. For Affymetrix platform, features are considered imported
     209        when the Affymetrix CDF file is actually uploaded.</para>
     210      <para>From the ArrayDesign Item View, click on the <guibutton>Import</guibutton>
     211      button</para>. <note>
     212        <para>The button only shows up if the logged in user has enough permissions.</para>
     213      </note>
     214      <para>A plugin interface is launched. One can either run the import using the autodetect
     215        settings or for more control, select a <guilabel>'Reporter Map Importer'</guilabel>
     216        plugin and then choose a <guilabel>plugin configuration</guilabel> available from
     217        the drop-down list populated from configurations shared to or owned by the user.</para>
     218      <para>BASE2 ships with Reporter Map Importer plugin configurations allowing to import
     219        features from Axon gal files and also gpr files (2 configurations_Block/Column/Row
     220        and Block/Row/Column for each file formats) and for Agilent FeatureExtraction files
     221        (to be confirmed). </para>
     222      <para>For more about the plugin configuration, refer to section <xref
     223          linkend="plugins.installation"/>.</para>
     224      <para>If the import run is successful, go to the ArrayDesign List view. The
     225          <guilabel>Has features</guilabel> column will show <guilabel>Yes (n)</guilabel>
     226        where n is the number of features actually present on the microarray and now
     227        associated to the newly created ArrayDesign.</para>
     228      <tip>
     229        <para>A list of Reporter Map Importer plugin configurations is maintained at BASE2
     230          site and each can be downloaded as xml file from <ulink url="tbd"/>.</para>
     231      </tip>
     232    </sect2>
     233    <para>If both actions have been successfully completed, the ArrayDesign is now fully defined
     234      and ArrayBatches and Array slides items can be created. This process is described in the
     235      following sections.</para>
     236
     237
     238    <sect2 id="array_lims.arraydesign.detail_view">
     239      <title>Viewing/Editing ArrayDesigns</title>
     240      <itemizedlist>
     241        <listitem>
     242          <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
     243              <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayDesign
     244            Item, which is a live link. </para>
     245        </listitem>
     246        <listitem>
     247          <para> Alternately, navigating to the ArrayDesign Item View, one can hit the
     248              <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
     249          <para>In both cases, an Edit pop-up windows opens. It is essentially identical
     250            to a Create window and allows updating information about a particular
     251            ArrayDesign item stored in BASE2.</para>
     252          <figure id="write_docbook_doc.figures.arraydesign-itemview">
     253            <title>ArrayDesign Item View</title>
     254            <screenshot>
     255              <mediaobject>
     256                <imageobject>
     257                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraydesign-itemview.png" format="PNG"/>
     258                </imageobject>
     259              </mediaobject>
     260            </screenshot>
     261          </figure>
     262        </listitem>
     263        <listitem>
     264          <para>From the ArrayDesign item View, all associated
     265            <guilabel>ArrayBatches</guilabel> are indicated as navigable links. Also
     266            present on the ArrayDesign Item View are the links back to
     267            <guilabel>Plates</guilabel> possibly used to define the ArrayDesign (none
     268            used in the screenshot).</para>
     269        </listitem>
     270      </itemizedlist>
     271    </sect2>
     272    <sect2 id="array_lims.arraydesign.delete">
     273      <title>Deleting/Restoring ArrayDesigns</title>
     274      <para>As for other items in BASE2, ArrayDesigns can be removed and restored. To do so,
     275        do the following:</para>
     276      <itemizedlist>
     277        <listitem>
     278          <para>Select one or more ArrayDesigns and click <guibutton>Delete</guibutton>
     279            button in the menu bar. </para>
     280          <para>All the selected ArrayDesigns have been marked as deleted and are no
     281            longer available from the interface. </para>
     282          <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
     283            select box the <guilabel>Removed</guilabel> option, one can see those of the
     284            ArrayDesigns earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
     285              <imageobject>
     286                <imagedata fileref="figures/deleted.gif" format="GIF"/>
     287              </imageobject>
     288            </inlinemediaobject> in front of them. </para>
     289        </listitem>
     290        <listitem>
     291          <para>Alternately, navigating to the ArrayDesign Item View, one can hit the
     292              <guibutton>Delete</guibutton> to performed the task. </para>
     293        </listitem>
     294        <listitem>
     295          <para>Deletion errors at this stage can be easily recovered. Select the item to
     296            recover from the List View (be sure to check the
     297            <guilabel>Removed</guilabel> option in the
     298            <guilabel>view/preset&hellip;</guilabel> filter) and hit the
     299              <guibutton>Restore</guibutton> button to performed the task. </para>
     300        </listitem>
     301      </itemizedlist>
     302      <important>
     303        <para>To really delete an item from the database you must use the trashcan. Items
     304          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     305          function, please refer to <xref linkend="trashcan"/>
     306        </para>
     307      </important>
     308    </sect2>
     309
     310  </sect1>
     311  <sect1 id="array_lims.arraybatch">
     312    <title>Managing Array Batches</title>
     313
     314    <sect2 id="array_lims.arraybatch.create">
     315      <title>Creating Array Batches </title>
     316      <para>In BASE2, Array Batches can be created by 2 routes:</para>
     317      <orderedlist>
     318        <listitem>
     319          <para>Creating Array Batch from the ArrayDesign List View page</para>
     320          <para>Clicking on the <inlinemediaobject>
     321              <imageobject>
     322                <imagedata fileref="figures/add.gif" format="GIF"/>
     323              </imageobject>
     324            </inlinemediaobject> add Array batch button available from the
     325              <guilabel>Batches</guilabel> column of the ArrayDesign list view page.
     326          </para>
     327        </listitem>
     328        <listitem>
     329          <para>Creating ArrayBatch from the ArrayBatch List View page</para>
     330          <para>Go to <menuchoice>
     331              <guimenu>View</guimenu>
     332              <guimenuitem>ArrayBatch</guimenuitem>
     333            </menuchoice></para>
     334          <para>Click on <guibutton>New&hellip;</guibutton> button </para>
     335        </listitem>
     336      </orderedlist>
     337
     338      <para>In both cases, an ArrayBatch Create pop-up window opens. The window contains 2
     339        mandatory fields:</para>
     340      <figure id="write_docbook_doc.figures.arraybatch-create">
     341        <title>Create New Array batch from the ArrayDesign List View</title>
     342        <screenshot>
     343          <mediaobject>
     344            <imageobject>
     345              <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-create.png" format="PNG"/>
     346            </imageobject>
     347          </mediaobject>
     348        </screenshot>
     349      </figure>
     350      <itemizedlist>
     351        <listitem>
     352          <para>
     353            <guilabel>Name</guilabel> and <guilabel>ArrayDesign</guilabel>.</para>
     354          <para>The later is a select-list population from ArrayDesigns owned by or shared
     355            to the user.</para>
     356        </listitem>
     357        <listitem>
     358          <para><guilabel>Print robot</guilabel> and <guilabel>Protocol</guilabel>, the
     359            other 2 fields, are optional and self explanatory.</para>
     360        </listitem>
     361      </itemizedlist>
     362      <para>Click on the <inlinemediaobject>
     363          <imageobject>
     364            <imagedata fileref="figures/save.gif" format="GIF"/>
     365          </imageobject>
     366        </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
     367          <imageobject>
     368            <imagedata fileref="figures/cancel.gif" format="GIF"/>
     369          </imageobject>
     370        </inlinemediaobject> button to abort.</para>
     371    </sect2>
     372
     373    <sect2 id="array_lims.arraybatch.detail_view">
     374      <title>Viewing/Editing ArrayBatches</title>
     375      <itemizedlist>
     376        <listitem>
     377          <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
     378              <keycap>SHIFT</keycap> keys while clicking on the name of an ArrayBatch
     379            Item, which is a live link. </para>
     380        </listitem>
     381        <listitem>
     382          <para> Alternately, navigating to the ArrayBatch Item View, one can hit the
     383              <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
     384          <para>In both cases, an Edit pop-up windows opens. It is essentially identical
     385            to a Create window and allows updating information about a particular
     386            ArrayBatch item stored in BASE2</para>
     387          <figure id="write_docbook_doc.figures.arraybatch-itemview">
     388            <title>ArrayBatch Item View</title>
     389            <screenshot>
     390              <mediaobject>
     391                <imageobject>
     392                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arraybatch-itemview.png" format="PNG"/>
     393                </imageobject>
     394              </mediaobject>
     395            </screenshot>
     396          </figure>
     397        </listitem>
     398        <listitem>
     399          <para>From the ArrayBatch item View, all associated <guilabel/>ArraySlides are
     400            indicated as their use in Hybridization events. Both ArraySlides and
     401            Hybridations are clickable items, enabling easy navigation.</para>
     402        </listitem>
     403      </itemizedlist>
     404    </sect2>
     405    <sect2 id="array_lims.arraybatch.delete">
     406      <title>Deleting/Restoring ArrayBatches</title>
     407      <para>As for other items in BASE2, ArrayBatches can be removed and restored. To do so,
     408        do the following</para>
     409      <itemizedlist>
     410        <listitem>
     411          <para>Select one or more ArrayBatches and click <guibutton>Delete</guibutton>
     412            button in the menu bar. </para>
     413          <para>All the selected ArrayBatches have been marked as deleted and are no
     414            longer available from the interface. </para>
     415          <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
     416            select box the <guilabel>Removed</guilabel> option, one can see those of the
     417            ArrayBatches earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
     418              <imageobject>
     419                <imagedata fileref="figures/deleted.gif" format="GIF"/>
     420              </imageobject>
     421            </inlinemediaobject> in front of them. </para>
     422        </listitem>
     423        <listitem>
     424          <para>Alternately, navigating to the ArrayBatch Item View, one can hit the
     425              <guibutton>Delete</guibutton> to performed the task. </para>
     426        </listitem>
     427        <listitem>
     428          <para>Deletion errors at this stage can be easily recovered. Select the item to
     429            recover from the List View (be sure to check the
     430            <guilabel>Removed</guilabel> option in the
     431            <guilabel>view/preset&hellip;</guilabel> filter) and hit the
     432              <guibutton>Restore</guibutton> button to performed the task. </para>
     433        </listitem>
     434      </itemizedlist>
     435      <important>
     436        <para>To really delete an item from the database you must use the trashcan. Items
     437          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     438          function, please refer to <xref linkend="trashcan"/>
     439        </para>
     440      </important>
     441    </sect2>
     442  </sect1>
     443  <sect1 id="array_lims.arrayslide">
     444    <title>Managing Array Slides</title>
     445    <sect2 id="array_lims.arrayslide.create">
     446      <title>Creating Array Slides </title>
     447      <para>In BASE2, Array Slides can be created by 2 routes:</para>
     448      <orderedlist>
     449        <listitem>
     450          <para>Creating Array Slides from the ArrayBatch View page</para>
     451          <para>Clicking on the <inlinemediaobject>
     452              <imageobject>
     453                <imagedata fileref="figures/add.gif" format="GIF"/>
     454              </imageobject>
     455            </inlinemediaobject> add Array slides button. </para>
     456          <figure id="write_docbook_doc.figures.arrayslide-single-create">
     457            <title>Create New Array Slide from the ArrayBatch List View</title>
     458            <screenshot>
     459              <mediaobject>
     460                <imageobject>
     461                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-single-create.png" format="PNG"/>
     462                </imageobject>
     463              </mediaobject>
     464            </screenshot>
     465          </figure>
     466        </listitem>
     467        <listitem>
     468          <para>Creating ArraySlides from the ArrayBatch List View page</para>
     469          <para>Go to <menuchoice>
     470              <guimenu>View</guimenu>
     471              <guimenuitem>ArraySlides</guimenuitem>
     472            </menuchoice></para>
     473          <para>Click on <guibutton>New&hellip;</guibutton> button </para>
     474        </listitem>
     475      </orderedlist>
     476
     477      <para>In both cases, an ArraySlide Create pop-up window opens. The window contains 2
     478        mandatory fields:</para>
     479      <itemizedlist>
     480        <listitem>
     481          <para>
     482            <guilabel>Name</guilabel> and <guilabel>ArrayBatch</guilabel>.</para>
     483          <para>The later is a select-list populated with ArrayBatches owned by or shared
     484            to the user.</para>
     485        </listitem>
     486        <listitem>
     487          <para><guilabel>Barcode</guilabel>, <guilabel>Index</guilabel> and
     488              <guilabel>Destroyed</guilabel>, a tick box enabling to record microarray
     489            slides lost by accident.</para>
     490        </listitem>
     491      </itemizedlist>
     492      <para>Click on the <inlinemediaobject>
     493          <imageobject>
     494            <imagedata fileref="figures/save.gif" format="GIF"/>
     495          </imageobject>
     496        </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
     497          <imageobject>
     498            <imagedata fileref="figures/cancel.gif" format="GIF"/>
     499          </imageobject>
     500        </inlinemediaobject> button to abort. </para>
     501
     502      <para> In addition to this classic way of creating BASE items, Arrays Slides can be
     503        created with a wizard available from both the ArraySlide Item view or from the
     504        ArrayBatch List View page. To call the wizard:</para>
     505      <para>Click on the <inlinemediaobject>
     506          <imageobject>
     507            <imagedata fileref="figures/new_wizard.gif" format="GIF"/>
     508          </imageobject>
     509        </inlinemediaobject> add multiple Array slides button in the
     510        <guilabel>Slides</guilabel> column of the ArrayBatch List view page.</para>
     511
     512      <para> or </para>
     513      <para>Click on the <inlinemediaobject>
     514          <imageobject>
     515            <imagedata fileref="figures/new_wizard.gif" format="GIF"/>
     516          </imageobject>
     517        </inlinemediaobject>
     518        <guibutton>Create multiple&hellip;</guibutton> button from the menu bar of the
     519        ArraySlides List View page </para>
     520
     521      <para>Either way ill open the a wizzard window as shown below</para>
     522      <figure id="write_docbook_doc.figures.arrayslide-multiple-create">
     523        <title>Create Muliple Array Slide from the ArrayBatch List View wizzard</title>
     524        <screenshot>
     525          <mediaobject>
     526            <imageobject>
     527              <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-multiple-create.png" format="PNG"/>
     528            </imageobject>
     529          </mediaobject>
     530        </screenshot>
     531      </figure>
     532      <para>Fill in the necessary information as exhaustively as possible.</para>
     533      <para>Click on the <inlinemediaobject>
     534          <imageobject>
     535            <imagedata fileref="figures/save.gif" format="GIF"/>
     536          </imageobject>
     537        </inlinemediaobject> Save button to store the information in BASE2 or on the <inlinemediaobject>
     538          <imageobject>
     539            <imagedata fileref="figures/cancel.gif" format="GIF"/>
     540          </imageobject>
     541        </inlinemediaobject> button to abort. </para>
     542    </sect2>
     543
     544    <sect2 id="array_lims.arrayslide.detail_view">
     545      <title>Viewing/Editing ArraySlides</title>
     546      <itemizedlist>
     547        <listitem>
     548          <para> Press and hold one of the <keycap>CTRL</keycap>, <keycap>ALT</keycap> or
     549              <keycap>SHIFT</keycap> keys while clicking on the name of an ArraySlide
     550            Item, which is a live link. </para>
     551        </listitem>
     552        <listitem>
     553          <para> Alternately, navigating to the ArraySlide Item View, one can hit the
     554              <guibutton>Edit&hellip;</guibutton> to performed the task.</para>
     555          <para>In both cases, an Edit pop-up windows opens. It is essentially identical
     556            to a Create window and allows updating information about a particular
     557            ArraySlide item stored in BASE2</para>
     558          <figure id="write_docbook_doc.figures.arrayslide-itemview">
     559            <title>ArraySlide Item View</title>
     560            <screenshot>
     561              <mediaobject>
     562                <imageobject>
     563                  <imagedata contentwidth="10cm" width="10cm" fileref="figures/arrayslide-itemview.png" format="PNG"/>
     564                </imageobject>
     565              </mediaobject>
     566            </screenshot>
     567          </figure>
     568        </listitem>
     569
     570        <listitem>
     571          <para>From the ArraySlide item View, the associated
     572            <guilabel>Hybridization</guilabel> can be indicated as navigable
     573          links</para>
     574        </listitem>
     575      </itemizedlist>
     576    </sect2>
     577    <sect2 id="array_lims.arrayslide.delete">
     578      <title>Deleting/Restoring ArraySlides</title>
     579      <para>As for other items in BASE2, ArraySlides can be removed and restored. To do so, do
     580        the following</para>
     581      <itemizedlist>
     582        <listitem>
     583          <para>Select one or more ArraySlides and click <guibutton>Delete</guibutton>
     584            button in the menu bar. </para>
     585          <para>All the selected ArraySlides have been marked as deleted and are no longer
     586            available from the interface. </para>
     587          <para>Only by selecting from the <guilabel>view/preset&hellip;</guilabel>
     588            select box the <guilabel>Removed</guilabel> option, one can see those of the
     589            ArraySlides earmarked for deletion. They will be shown with a symbol <inlinemediaobject>
     590              <imageobject>
     591                <imagedata fileref="figures/deleted.gif" format="GIF"/>
     592              </imageobject>
     593            </inlinemediaobject> in front of them. </para>
     594        </listitem>
     595        <listitem>
     596          <para>Alternately, navigating to the ArraySlide Item View, one can hit the
     597              <guibutton>Delete</guibutton> to performed the task. </para>
     598        </listitem>
     599        <listitem>
     600          <para>Deletion errors at this stage can be easily recovered. Select the item to
     601            recover from the List View (be sure to check the
     602            <guilabel>Removed</guilabel> option in the
     603            <guilabel>view/preset&hellip;</guilabel> filter) and hit the
     604              <guibutton>Restore</guibutton> button to performed the task. </para>
     605        </listitem>
     606      </itemizedlist>
     607      <important>
     608        <para>To really delete an item from the database you must use the trashcan. Items
     609          deleted from the Trashcan can not be recovered. To learn more about the trashcan
     610          function, please refer to <xref linkend="trashcan"/>
     611        </para>
     612      </important>
     613    </sect2>
     614
     615
     616  </sect1>
     617
    36618</chapter>
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