Changeset 286


Ignore:
Timestamp:
May 22, 2007, 3:20:07 PM (16 years ago)
Author:
Jari Häkkinen
Message:

Fixes #42.

File:
1 edited

Legend:

Unmodified
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  • trunk/se/lu/thep/affymetrix/README

    r285 r286  
    2828== About se.lu.thep.affymetrix package ==
    2929
     30''A short diversion before we proceed, this paragraph is aimed at
     31people starting with an empty BASE server. The default BASE
     32installation comes set up to store the same reporter (probeset)
     33information as BASE 1.2.x do. This set up is not optimal for
     34Affymetrix data but can still be used. In order to understand how to
     35define what reporter information is stored in BASE and how to change
     36what is stored, you may want to visit
     37http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html
     38before you start using your shiny BASE installation.''
     39
    3040Send comments, suggestion, complaints, or questions regarding this
    3141package to the
     
    3747The RMAExpress plug-in is installed in the
    3848[http://base2.thep.lu.se:8080/demo BASE2 demo server].
    39 
    4049
    4150For installation or updating instructions please see file INSTALL.
     
    8796    privileges, an ordinary BASE user does NOT have this privilege.
    8897
    89     There is more than one way to create plug-in configurations. Here
    90     we outline the most straightforward route. There is a chapter in
    91     the BASE manual devoted for plug-in installation, follow the link
    92     above to find the document.
     98 There is more than one way to create plug-in configurations. Here we
     99 outline the most straightforward route. There is a chapter in the
     100 BASE manual devoted for plug-in installation, follow the link above
     101 to find the document.
    93102
    94103    - First you need to create an plug-in configuration for the
     
    118127      'Next'. Set the 'Update existing reporters' to "true" if an
    119128      update of already stored reporter information is wanted. Start
    120       the import by clicking 'Next' in the parameter dialog
     129      the import by clicking 'Next' in the parameter dialog.
    121130
    122    The reporter information is now in the database. You may delete the
    123    AffyChip_annot.csv file from BASE if you wish, it is not needed
    124    anymore. You may want to update reporter information when
    125    Affymetrix releases a new version of their annotation but remember
    126    there is no versioning for this type of information in BASE. If you
    127    update reporter information you only need to redo the last step.
     131 The reporter information is now in the database. You may delete the
     132 AffyChip_annot.csv file from BASE if you wish, it is not needed
     133 anymore. You may want to update reporter information when Affymetrix
     134 releases a new version of their annotation but remember there is no
     135 versioning for this type of information in BASE. If you update
     136 reporter information you only need to redo the last step.
    128137
    129  3. You need to define the design of the AffyChip in BASE, i.e. import
    130     the AffyChip.cdf file. This is only needed to do once for every
    131     AffyChip design to be added into BASE. This step can only be
    132     performed by a user with array LIMS administrative (create)
    133     privileges, an ordinary BASE user does NOT have this privilege.
     138 3. You need to define the design of the !AffyChip in BASE,
     139    i.e. import the !AffyChip.cdf file. This is only needed to do once
     140    for every !AffyChip design to be added into BASE. This step can
     141    only be performed by a user with array LIMS administrative
     142    (create) privileges, an ordinary BASE user does NOT have this
     143    privilege.
    134144
    135145    - Define a new array design through 'Array LIMS' -> 'Array
     
    174184
    175185 7. You made it here. This means that the plug-in works and you are
    176     ready to start using BASE. The get the most out of BASE you should
    177     now read the BASE manual and documentation available at
    178     http://base.thep.lu.se/wiki/Manuals
     186    ready to start using BASE. The get the most out of BASE you should
     187    now read the BASE manual and documentation available at
     188    http://base.thep.lu.se/wiki/Manuals
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