Changeset 5783


Ignore:
Timestamp:
Oct 5, 2011, 12:34:24 PM (11 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

Experiments and analysis chapter.

Location:
trunk/doc/src/docbook/user
Files:
5 edited
2 moved

Legend:

Unmodified
Added
Removed

  • trunk/doc/src/docbook/user/analysis.xml

    r5774 r5783  
    2626
    2727<sect1 id="experiments_analysis.analysis">
     28  <?dbhtml filename="analysis.html" ?>
    2829  <title>Analysing data within BASE</title>
    2930  <para>TODO</para>

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

    r5738 r5783  
    155155      </sect3>
    156156
    157       <sect3 id="array_lims.arraydesign.properties.annotations">
     157      <sect3 id="array_lims.arraydesign.datafiles">
     158        <title>Data files</title>
     159        <para>
     160          This allows you to select files that contain data for the array design.
     161          Read more about this in <xref linkend="platforms.selectfiles" />.
     162        </para>
     163      </sect3>
     164     
     165      <sect3 id="array_lims.arraydesign.annotations">
    158166        <title>Annotations and inherited annotations</title>
    159167        <para>

  • trunk/doc/src/docbook/user/derivedbioassays.xml

    r5774 r5783  
    2424  along with BASE. If not, see <http://www.gnu.org/licenses/>.
    2525-->
    26 <sect1 id="experiments_analysis.scans">
    27   <title>Scans and images</title>
     26<sect1 id="experiments_analysis.derivedbioassays">
     27  <?dbhtml filename="derivedbioassays.html" ?>
     28 
     29  <title>Derived bioassays</title>
    2830  <para>
    29     When you have done your hybridization and scanned it,
    30     you can register information about the scanning process
    31     as a <guilabel>Scan</guilabel> item in BASE. A scan
    32     item holds information about the scanning process,
    33     such as which scanner and what settings you have
    34     used. It can also hold information about the images
    35     that was produced as well as the actual image files.
     31    When you have processed your physical bioassay you can
     32    register any information that you have gathered as
     33    <guilabel>Derived bioassay</guilabel> items in BASE.
     34    The derived bioassay can represent both a physical process,
     35    such as scanning a microarray slide, or a software
     36    process such as aligning sequence data against a reference
     37    genome. It is even possible to register child derived
     38    bioassays if there are multiple steps involved that you want
     39    to register independently. Each derived bioassay can
     40    specify a protocol (with parameters if needed) and a hardware
     41    or software item that was used to create it.
    3642  </para>
    3743 
     44  <para>
     45    It is also possible to link one or more files to the derived
     46    bioassay. This feature requires that a subtype is selected and
     47    that the subtype has been linked with the file types that
     48    are useful in that context. For example, the <guilabel>Scan</guilabel>
     49    subtype is linked with <guilabel>Image</guilabel> files.
     50  </para>
     51 
    3852  <note>
    39     A scan does not have information about the spots or
    40     raw data. The process of analysing the images is
    41     considered a separate step. This information is held
    42     by raw bioassays.
     53    <para>
     54    A derived bioassay can only hold data in the form of files.
     55    When the data has been processed enough to make it a sensible
     56    option (performance-wise) to import into the database a
     57    <guilabel>Raw bioassay</guilabel> should be created.
     58    </para>
    4359  </note>
    4460 
    45   <sect2 id="experiment_analysis.scans.properties">
    46     <title>Scan properties</title>
    47    
     61  <sect2 id="experiments_analysis.derivedbioassays.create">
     62    <title>Create derived bioassays</title>
     63 
    4864    <para>
    49       A scan has the following properties:
     65      Beside the common way, using the &gbNew; button, a derived bioassay can be created in one of
     66      the following ways:
    5067    </para>
    51    
    52     <helptext external_id="scan.edit" title="Edit scan">
     68      <variablelist>
     69        <varlistentry>
     70          <term>from either physical bioassay list- or single view- page.</term>
     71          <listitem>
     72            <para>
     73              A derived bioassay must always have a physical bioassay as it's
     74              parent. Therefore, a natural way to create a derived bioassay is to click on
     75              <guiicon>
     76                <inlinemediaobject>
     77                  <imageobject>
     78                    <imagedata fileref="figures/add.png" format="PNG" />
     79                  </imageobject>
     80                </inlinemediaobject>
     81              </guiicon>
     82              in the <guilabel>Derived bioassays</guilabel> column in the list view. There is also a
     83              corresponding button, <guibutton>New derived bioassay&hellip;</guibutton>
     84              in the toolbar when viewing a single physical bioassay.
     85            </para>
     86          </listitem>
     87        </varlistentry>
     88        <varlistentry>
     89          <term>from either derived bioassays list- or single view- page</term>
     90          <listitem>
     91            <para>
     92              A child derived bioassay must always have another derived bioassay
     93              as it's parent. Click on the
     94              <guiicon>
     95                <inlinemediaobject>
     96                  <imageobject>
     97                    <imagedata fileref="figures/add.png" format="PNG" />
     98                  </imageobject>
     99                </inlinemediaobject>
     100              </guiicon> icon in the <guilabel>Child bioassays</guilabel> column
     101              to create a new child derived bioassay. There is also a
     102              corresponding button, <guibutton>New child bioassay&hellip;</guibutton>
     103              in the toolbar when viewing a single derived bioassay.
     104            </para>
     105          </listitem>
     106        </varlistentry>
     107      </variablelist>
     108  </sect2>
     109 
     110  <sect2 id="experiment_analysis.derivedbioassay.properties">
     111    <title>Derived bioassay properties</title>
     112   
     113    <para>
     114      A derived bioassay has the following properties:
     115    </para>
     116   
     117    <helptext external_id="derivedbioassay.edit" title="Edit derived bioassay">
    53118    <variablelist>
    54119      <varlistentry>
    … …  
    56121        <listitem>
    57122          <para>
    58             The name of the scan.
    59           </para>
    60         </listitem>
    61       </varlistentry>
    62       <varlistentry>
    63         <term><guilabel>Hybridization</guilabel></term>
    64         <listitem>
    65           <para>
    66             The hybridization this scan comes from.
    67           </para>
    68         </listitem>
    69       </varlistentry>
    70       <varlistentry>
    71         <term><guilabel>Scanner</guilabel></term>
    72         <listitem>
    73           <para>
    74             The scanner that was used (optional).
     123            The name of the derived bioassay.
     124          </para>
     125        </listitem>
     126      </varlistentry>
     127      <varlistentry>
     128        <term><guilabel>Type</guilabel></term>
     129        <listitem>
     130          <para>
     131            The subtype of the derived bioassay. The list may evolve depending on additions by
     132            the server administrator. Selecting the proper subtype is required
     133            to be able to attach data files to the bioassay. It will also help BASE
     134            to automatically guess the most likely subtype when creating child bioassays.
     135            <nohelp>
     136            See <xref linkend="subtypes" /> for more information.
     137            </nohelp>
     138          </para>
     139        </listitem>
     140      </varlistentry>
     141      <varlistentry>
     142        <term><guilabel>Parent type</guilabel></term>
     143        <listitem>
     144          <para>
     145            Select if the parent item is a physical bioassay or
     146            another derived bioassay. This option is only available when creating new
     147            derived bioassays. Once created it is not possible to change
     148            the parent.
     149          </para>
     150        </listitem>
     151      </varlistentry>
     152      <varlistentry>
     153        <term><guilabel>Extract</guilabel></term>
     154        <listitem>
     155          <para>
     156            Select the extract that this derived bioassay is linked with. The list
     157            contains all the extracts that are present on the physical bioassay.
     158            Do not select an extract if the derived bioassay represents more than
     159            one extract at this stage.
    75160          </para>
    76161        </listitem>
    … …  
    80165        <listitem>
    81166          <para>
    82             The protocol used for scanning (optional). Scanning
    83             parameters may be registered as part of
    84             the protocol.
     167            The protocol used in the process that created this derived bioassay (optional).
     168            Parameters may be registered as part of the protocol.
     169          </para>
     170        </listitem>
     171      </varlistentry>
     172      <varlistentry>
     173        <term><guilabel>Hardware</guilabel></term>
     174        <listitem>
     175          <para>
     176            The machine used in the process that created this derived bioassay (optional).
     177          </para>
     178        </listitem>
     179      </varlistentry>
     180      <varlistentry>
     181        <term><guilabel>Software</guilabel></term>
     182        <listitem>
     183          <para>
     184            The software used in the process that created this derived bioassay (optional).
    85185          </para>
    86186        </listitem>
    … …  
    90190        <listitem>
    91191          <para>
    92             A decription of the scan (optional).
     192            A decription of the derived bioassay (optional).
    93193          </para>
    94194        </listitem>
    … …  
    97197   
    98198    <seeother>
     199      <other external_id="datafiles.edit">Data files</other>
    99200      <other external_id="annotations.edit">Annotations</other>
    100201      <other external_id="annotations.edit.inerited">Inherit annotations</other>
    … …  
    103204    </helptext>
    104205   
    105     <para>
    106       A scan can have annotations. Read more about this in
    107       <xref linkend="annotations"/>.
    108     </para>
     206    <sect3 id="experiment_analysis.derivedbioassay.datafiles">
     207      <title>Data files</title>
     208      <para>
     209        This allows you to select files that contain data for the derived bioassay.
     210        Read more about this in <xref linkend="platforms.selectfiles" />.
     211      </para>
     212    </sect3>
     213   
     214    <sect3 id="experiment_analysis.derivedbioassay.annotations">
     215      <title>Annotations and inherited annotations</title>
     216      <para>
     217        This allows you to input values associated to annotation types devised to refine
     218        the description. Read more about annotations in
     219        <xref linkend="annotations" />.
     220      </para>
     221    </sect3>
    109222   
    110223  </sect2>
    111  
    112   <sect2 id="experiment_analysis.scans.images">
    113     <title>Images</title>
    114    
    115     <para>
    116       If you want you can upload the images from the scan
    117       to BASE. This is optional, but the images
    118       are needed if you want to create spot images later
    119       on.
    120     </para>
    121    
    122     <para>
    123       To upload images for a scan you must first go to
    124       the single-item view for the scan. On this page
    125       you will find the <guilabel>Images</guilabel>
    126       tab which will take you to a list view
    127       of the images from this scan. New images are created
    128       in the same way as any other item in BASE,
    129       by clicking the <guilabel>New&hellip;</guilabel> button.
    130       You may add as many images as you like.
    131     </para>
    132    
    133     <para>
    134       An image has the following properties:
    135     </para>
    136 
    137     <helptext external_id="image.edit" title="Edit image">
    138    
    139     <variablelist>
    140       <varlistentry>
    141         <term><guilabel>Name</guilabel></term>
    142         <listitem>
    143           <para>
    144             The name of the image. The name is automatically
    145             generated from the name of the scan, but you may
    146             enter a different name.
    147           </para>
    148         </listitem>
    149       </varlistentry>
    150       <varlistentry>
    151         <term><guilabel>File</guilabel></term>
    152         <listitem>
    153           <para>
    154             The file containing the actual
    155             image data (optional). Use the <guibutton>Select</guibutton>
    156             button to select an existing file or upload a new
    157             one.
    158           </para>
    159         </listitem>
    160       </varlistentry>
    161       <varlistentry>
    162         <term><guilabel>Format</guilabel></term>
    163         <listitem>
    164           <para>
    165             The image format (optional). You can select between
    166             <emphasis>TIFF</emphasis>, <emphasis>JPEG</emphasis>
    167             and <emphasis>Unknown</emphasis>.
    168           </para>
    169         </listitem>
    170       </varlistentry>
    171       <varlistentry>
    172         <term><guilabel>Preview</guilabel></term>
    173         <listitem>
    174           <para>
    175             If the image is a preview image or the full
    176             scan.
    177           </para>
    178         </listitem>
    179       </varlistentry>
    180       <varlistentry>
    181         <term><guilabel>Description</guilabel></term>
    182         <listitem>
    183           <para>
    184             A description of the image (optional).
    185           </para>
    186         </listitem>
    187       </varlistentry>
    188     </variablelist>
    189     </helptext>       
    190    
    191   </sect2>
     224
    192225 
    193226</sect1>

  • trunk/doc/src/docbook/user/experiments.xml

    r5682 r5783  
    2626
    2727<sect1 id="experiments_analysis.experiments">
     28  <?dbhtml filename="experiments.html" ?>
    2829  <title>Experiments</title>
    2930  <para>
    3031    Experiments are the starting point for analysis. When you have
    3132    uploaded and imported your raw data, collected and registered all
    32     information and annotations about samples, hybridizations, and other
     33    information and annotations about samples, bioassays, and other
    3334    items, it is time to collect everything in an experiment.
    3435  </para>
    … …  
    146147            <para>
    147148              The ID of the publication in the
    148               <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query/static/overview.html"
     149              <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/"
    149150                >PubMed</ulink> database.
    150151            </para>

  • trunk/doc/src/docbook/user/experiments_analysis.xml

    r5782 r5783  
    2929
    3030  <title>Experiments and analysis</title>
    31   <include file="scans_images.xml"/>
     31  <include file="derivedbioassays.xml"/>
    3232  <include file="rawbioassays.xml"/>
    3333  <include file="experiments.xml"/>
    34   <include file="analyse_in_base.xml"/>
     34  <include file="analysis.xml"/>
    3535</chapter>

  • trunk/doc/src/docbook/user/platforms.xml

    r5738 r5783  
    227227    </helptext>
    228228   
    229     <sect2 id="platforms.variants">
    230       <title>Platform variants</title>
    231 
    232       <para>
    233         It is possible for an administrator to define variants of
    234         a platform. The main purpose for this is to be able to
    235         select additional file types that are only used in some cases.
    236         The file types defined by the parent platform are always inherited
    237         by the variants.
    238       </para>
    239      
    240       <para>
    241         You can create new variants from the single-item view
    242         of a platform. This view also has a <guilabel>Variants</guilabel>
    243         tab which lists all variants that has been defined for a platform.
    244       </para>
    245      
    246     </sect2>
     229  </sect1>
     230
     231  <sect1 id="platforms.variants">
     232    <title>Platform variants</title>
     233
     234    <para>
     235      It is possible for an administrator to define variants of
     236      a platform. The main purpose for this is to be able to
     237      select additional file types that are only used in some cases.
     238      The file types defined by the parent platform are always inherited
     239      by the variants.
     240    </para>
     241   
     242    <para>
     243      You can create new variants from the single-item view
     244      of a platform. This view also has a <guilabel>Variants</guilabel>
     245      tab which lists all variants that has been defined for a platform.
     246    </para>
    247247   
    248248  </sect1>
    … …  
    388388    </helptext>     
    389389
    390     <helptext external_id="datafiles.edit" title="Data files" webonly="1">
     390  </sect1>
     391 
     392  <sect1 id="platforms.selectfiles">
     393    <title>Selecting files for an item</title>
     394
     395    <para>
     396      Selecting files for an item follows the same pattern
     397      for all items that supports it. They all have a
     398      <guilabel>Data files</guilabel> tab in their edit view.
     399      On this tab you can select files for all file types
     400      that are defined by the platform or subtype of the item.
     401    </para>
     402
     403    <figure
     404      id="platforms.figures.selectfiles">
     405      <title>Selecting files for an array design</title>
     406      <screenshot>
     407        <mediaobject>
     408          <imageobject>
     409            <imagedata
     410              fileref="figures/select_files.png" format="PNG" />
     411          </imageobject>
     412        </mediaobject>
     413      </screenshot>
     414    </figure>
     415
     416    <helptext external_id="datafiles.edit" title="Data files">
    391417      <para>
    392       On this tab you can select files for each of the file types
    393       defined by the platform you selected on the <guilabel>Properties</guilabel>
    394       tab. You may enter the path manually for each file or you can use the
    395       &gbBrowse; button to select a file from the file manager.
     418      The list contains all file types that are defined by by the platform or subtype that
     419      is selected on the <guilabel>Properties</guilabel>
     420      tab. Use the &gbBrowse; or <guibutton>Add</guibutton> icons to select files from
     421      the file manager. Note that for some file types only a single file can be selected,
     422      but for other file types multiple files are allowed. The dropdown list contains
     423      recently used files as well as an option to clear the selected file.
    396424      </para>
    397425     
    398426      <variablelist>
    399427      <varlistentry>
    400         <term><guilabel>Validate</guilabel></term>
     428        <term><guilabel>Validate files</guilabel></term>
    401429        <listitem>
    402430          <para>
    403431            Mark this checkbox if you want to validate and extract metadata
    404432            from the selected files. The checkbox is automatically checked
    405             if you remove or select a different file.
     433            if changes are made.
    406434          </para>
    407435        </listitem>
    … …  
    419447     
    420448    </helptext>
    421 
    422449  </sect1>
    423450

  • trunk/doc/src/docbook/user/rawbioassays.xml

    r4568 r5783  
    2626
    2727<sect1 id="experiments_analysis.rawbioassay">
     28  <?dbhtml filename="rawbioassays.html" ?>
    2829  <title>Raw bioassays</title>
    2930  <para>
    3031    A <guilabel>Raw bioassay</guilabel> is the representation
    31     of the result of analysing one or more images from a
    32     <guilabel>Scan</guilabel>. This typically generates a
    33     raw data file with lots of measurements for the spots
    34     on the hybridization.
     32    of the result of analyzing data from the physical bioassay
     33    down to the point where we have a file or a set of files
     34    containing measurements per feature (eg. spot, gene, etc.)
     35    for a single sample or extract. Further analysis is usually
     36    needed before we can say something about individual features
     37    or samples and how they relate to each other. This
     38    kind of analisys is done in <guilabel>Experiments</guilabel>.
     39    See <xref linkend="experiments_analysis.experiments" />.
    3540  </para>
    3641 
    3742  <para>
    38     Creating a new raw bioassay is a two- or three-step process:
     43    The term <guilabel>Raw bioassay</guilabel> is bit misleading since the
     44    real "raw data" is actually the images from a microarray scan or the
     45    output from a sequencer. For historical reasons we have chosen to keep
     46    the term raw bioassay since this represents the first possibility for
     47    a transition between file-base data and database-stored data. Typically,
     48    all pre-rawbioassay analysis is done outside of BASE, and although
     49    we now have the possibility to track this in detail, it will
     50    probably remain so for some time in the future. See
     51    <xref linkend="experiments_analysis.derivedbioassays" />.
     52 
    3953  </para>
    4054 
    41   <orderedlist>
    42     <listitem>
    43       <para>
    44         Create a new raw bioassay item with the
    45         <guilabel>New</guilabel> button in the
    46         list view.
    47       </para>
    48     </listitem>
    49     <listitem>
    50       <para>
    51       Upload the file(s) with the raw data and attach it/them to the
    52       raw bioassay.
    53       </para>
    54     </listitem>
    55     <listitem>
    56       <para>
    57         The used platform may require that data is imported to the database.
    58         See <xref linkend="import_data" />. If the platform is a
    59         file-only platform, this step can be skipped.
    60       </para>
    61     </listitem>
    62   </orderedlist>
    63  
    64   <note>
    65     <title>Supported file formats</title>
    66     BASE has built-in support for most file formats where the data comes
    67     in a tab-separated (or similar) form. Data from one hybridization
    68     must be in a single file. Support for other file formats
    69     may be added through plug-ins.
    70   </note>
     55  <sect2 id="experiments_analysis.rawbioassay.create">
     56    <title>Create raw bioassays</title>
     57    <para>
     58      Creating a new raw bioassay is a two- or three-step process:
     59    </para>
     60 
     61    <orderedlist>
     62      <listitem>
     63        <para>
     64          Create a new raw bioassay item with the &gbNew; button in the raw bioassays list view.
     65          It is also possible to create raw bioassays from the derived bioassays
     66          list- and single view- page.
     67        </para>
     68      </listitem>
     69      <listitem>
     70        <para>
     71        Upload the file(s) with the raw data and attach them to the
     72        raw bioassay.
     73        </para>
     74      </listitem>
     75      <listitem>
     76        <para>
     77          The used platform may require that data is imported to the database.
     78          See <xref linkend="import_data" />. If the platform is a
     79          file-only platform, this step can be skipped.
     80        </para>
     81      </listitem>
     82    </orderedlist>
     83 
     84    <note>
     85      <title>Supported file formats</title>
     86      BASE has built-in support for most file formats where the data comes
     87      in a tab-separated (or similar) form. Data for one raw bioassay
     88      must be in a single file. Support for other file formats
     89      may be added through plug-ins.
     90    </note>
     91  </sect2>
    7192 
    7293  <sect2 id="experiments_analysis.rawbioassay.properties">
    … …  
    99120      <varlistentry>
    100121        <term>
    101           <guilabel>Array index</guilabel>
    102         </term>
    103         <listitem>
    104           <para>
    105             The index of the sub-array on the hybridization this
    106             raw bioassay's data is linked with. The default value
    107             is 1. With some platforms, for example Illumina, which has
    108             slides with 6 or 8 arrays the value should be changed to
    109             reflect the correct sub-array. This information is important
    110             to link the raw bioassay with the correct biomaterial
    111             entries.
    112           </para>
    113         </listitem>
    114       </varlistentry>
    115       <varlistentry>
    116         <term>
    117122          <guilabel>Platform</guilabel>
    118123        </term>
    … …  
    136141            imported. <nohelp>See
    137142            <xref linkend="experiments_analysis.rawdatatypes" />.</nohelp>
     143          </para>
     144        </listitem>
     145      </varlistentry>
     146      <varlistentry>
     147        <term><guilabel>Parent bioassay</guilabel></term>
     148        <listitem>
     149          <para>
     150            The derived bioassay that is the parent of this
     151            raw bioassay.
     152          </para>
     153        </listitem>
     154      </varlistentry>
     155      <varlistentry>
     156        <term><guilabel>Parent extract</guilabel></term>
     157        <listitem>
     158          <para>
     159            The extract which this raw bioassay has measured. This is normally selected
     160            among the extracts that are linked with the physical bioassay that this
     161            raw bioassay is coming from. Selecting the correct extract is important if the
     162            physical bioassay contains more than one extract, since otherwise it may affect
     163            how annotations are inherited and used in downstream analysis.
    138164          </para>
    139165        </listitem>
    … …  
    186212      </varlistentry>
    187213      <varlistentry>
    188         <term><guilabel>Scan</guilabel></term>
    189         <listitem>
    190           <para>
    191             The scan this raw bioassay is related to (optional). Changing this property will
    192             also update the value in <guilabel>Array design</guilabel>, but only if the
    193             selected scan is connected to an array design and the current user has permission
    194             to view it.
    195           </para>
    196         </listitem>
    197       </varlistentry>
    198       <varlistentry>
    199214        <term><guilabel>Software</guilabel></term>
    200215        <listitem>
    201216          <para>
    202             The software used to analyse the image or images (optional).
     217            The software used to generate the raw data (optional).
    203218          </para>
    204219        </listitem>
    … …  
    208223        <listitem>
    209224          <para>
    210             The protocol used when analysing the image(s) (optional).
     225            The protocol used when generating the raw data (optional).
    211226            Software parameters may be registered as part of
    212227            the protocol.
    … …  
    231246    </helptext>
    232247       
    233     <para>
    234       A raw bioassay can have annotations. Read more about this in
    235       <xref linkend="annotations"/>.
    236     </para>
     248    <sect3 id="experiment_analysis.rawbioassay.datafiles">
     249      <title>Data files</title>
     250      <para>
     251        This allows you to select files that contain data for the raw bioassay.
     252        Read more about this in <xref linkend="platforms.selectfiles" />.
     253      </para>
     254    </sect3>
     255   
     256    <sect3 id="experiment_analysis.rawbioassay.annotations">
     257      <title>Annotations and inherited annotations</title>
     258      <para>
     259        This allows you to input values associated to annotation types devised to refine
     260        the description. Read more about annotations in
     261        <xref linkend="annotations" />.
     262      </para>
     263    </sect3>
    237264   
    238265  </sect2>
    … …  
    257284      <title>File-only platforms</title>
    258285      File-only platforms, such as Affymetrix, is handled differently and data is not
    259       imported into the database. See <xref linkend="experiments_analysis.fileonly" />.
     286      imported into the database.
    260287    </note>
    261288   
    … …  
    267294    <para>
    268295      A raw data type defines the types of measured values that can be stored
    269       for individual spots in the database. Usually this includes some
     296      for individual features in the database. Usually this includes some
    270297      kind of foreground and background intensity values. The number and meaning
    271       of the values usually depends on the scanner and software used to analyse
    272       the images from a hybridization. Many tools provide mean and median values,
     298      of the values usually depends on the hardware and software used to analyze
     299      the data from the experiment. Many tools provide mean and median values,
    273300      standard deviations, quality control information, etc. Since there are so
    274301      many existing tools with many different data file formats BASE uses a
    … …  
    284311      <title>File-only platforms</title>
    285312      <para>
    286         BASE 2.5 introduced a generic way to keep the data in files instead
    287         of having to import it to the database. In older BASE versions this
    288         ability was limited to the Affymetrix platform. The reason for
    289         keeping the data in files is that the number of spots tend to grow,
    290         which may result in bad performance if the database should be used.
    291         A typical Genepix file contains ~55K spots while an Affymetrix file may
    292         have millions.
     313        In some cases it doesn't make sense to import any data into the
     314        database. The main reason is that performance will suffer as the
     315        number of entries in the database gets higher. A typical Genepix file
     316        contains ~55K spots while an Affymetrix file may have millions.
    293317      </para>
    294318      <para>
    … …  
    315339    <title>Spot images</title>
    316340    <para>
    317       If you have uploaded the image or images from the scan
    318       you may create spot images. Spot images allows you to
    319       view the image of each spot separately in the analysis.
    320       For this to work the raw data must contain the X and Y
     341      This section only applies to microarray platforms where
     342      a coordinate system is used to identify spots on the
     343      array slides. The raw data must contain X and Y
    321344      coordinates of each spot.
    322345    </para>
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