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Timestamp:
May 22, 2007, 2:51:46 PM (16 years ago)
Author:
Jari Häkkinen
Message:

Addresses #42.

File:
1 edited

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

    r279 r285  
    44{{{
    55Copyright (C) 2006 Jari Häkkinen
    6 Copyright (C) 2007 Peter Johansson
     6Copyright (C) 2007 Jari Häkkinen, Peter Johansson
    77
    88This file is part of se.lu.thep.affymetrix package for BASE,
    … …  
    2626----------------------------------------------------------------------
    2727
    28 = About se.lu.thep.affymetrix package =
     28== About se.lu.thep.affymetrix package ==
    2929
    3030Send comments, suggestion, complaints, or questions regarding this
    31 package to the [http://base.thep.lu.se/wiki/MailingLists BASE mailing
    32 lists].
     31package to the
     32[http://base.thep.lu.se/wiki/MailingLists BASE mailing lists].
    3333
    3434This file contains information on se.lu.thep.affymetrix package. This
    3535package contains the RMAExpress and Plier plug-ins.
    3636
    37 The RMAExpress plug-in is installed in the BASE2 demo server
    38 (http://base2.thep.lu.se:8080/demo).
     37The RMAExpress plug-in is installed in the
     38[http://base2.thep.lu.se:8080/demo BASE2 demo server].
    3939
    4040
    … …  
    4242
    4343
    44 What is RMAExpress and Plier plug-ins for BASE?
     44== What is RMAExpress and Plier plug-ins for BASE? ==
    4545
    4646RMAExpress and Plier are two similar plug-ins needed to make use of
    … …  
    5050imported into BASE.
    5151
    52 These plug-ins do not implement the RMA method and Plier method,
    53 but rather rely on third-party binary packages.
     52These plug-ins do not implement the RMA method and Plier method, but
     53rather rely on third-party binary packages for the algorithm
     54implementations.
    5455
    5556The RMAExpress plug-in relies on RMAExpressConsole available in the
    … …  
    5859information please refer to the RMAExpress web site. In short RMA is
    5960the Robust Multichip Average. It consists of three steps: a background
    60 adjustment, quantile normalization, and finally a summarization.
     61adjustment, quantile normalization, and finally a summarizing.
    6162
    6263The Plier plug-in relies on `apt-probeset-summarize` included in
    … …  
    6869refer to the Affymetrix home page.
    6970
    70 What is required to use the these plug-ins for BASE? The "BASE
    71 getting started document" may also be helpful,
    72 http://base.thep.lu.se/chrome/site/doc/user/getting_started.html
    7371
    74   1. You need to install the plug-in and make BASE aware of the new
    75      plugin, see INSTALL for instruction for installation
    76      instructions.
     72== What is required for use of these plug-ins for BASE? ==
    7773
    78   2. You need to import probe set information into BASE (reporter
    79      information), i.e. import AffyChip_annot.csv into BASE. This is
    80      only needed to do once, and optionally later if reporter
    81      information should be updated. This step can only be performed by a
    82      user with reporter administrative (create) privileges, an ordinary
    83      BASE user does NOT have this privilege.
     74This section is a short introduction to get going with the plug-ins
     75and Affymetrix data in BASE. More documentation is available at
     76http://base.thep.lu.se/wiki/Manuals and you should read them to learn
     77how to use BASE.
     78
     79 1. You need to install the plug-in and make BASE aware of the new
     80    plug-in, see INSTALL for instruction for installation instructions.
     81
     82 2. You need to import probe set information into BASE (reporter
     83    information in BASE language), i.e. import AffyChip_annot.csv into
     84    BASE. This is only needed to do once, and optionally later if
     85    reporter information should be updated. This step can only be
     86    performed by a user with reporter administrative (create)
     87    privileges, an ordinary BASE user does NOT have this privilege.
     88
     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.
    8493
    8594    - First you need to create an plug-in configuration for the
    … …  
    91100    - A 'Parser settings' dialog will appear. Set fields according to
    92101      this list:
    93 
     102{{{
    94103  Data header  : "Probe Set ID","GeneChip Array",.*
    95104  Data splitter: (?!"),(?=")
    … …  
    97106  Name         : \Probe Set ID\
    98107  Reporter ID  : \Probe Set ID\
    99 
    100       Finalize by clicking 'Next'.
     108}}}
     109      Finalize by clicking 'Next'. Note, the above example will
     110      perform a minimalistic import of annotation information, please
     111      read the BASE documentation on how to import more probeset
     112      related information. However, don't worry about that now, you
     113      can always fix the annotation later.
    101114
    102115    - Import the reporters by choosing 'View' -> 'Reporters' and the
    … …  
    114127   update reporter information you only need to redo the last step.
    115128
    116 3) You need to define the design of the AffyChip in BASE, i.e. import
    117    the AffyChip.cdf file. This is only needed to do once for every
    118    AffyChip design to be added into BASE. This step can only be
    119    performed by a user with array LIMS administrative (create)
    120    privileges, an ordinary BASE user does NOT have this privilege.
     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.
    121134
    122135    - Define a new array design through 'Array LIMS' -> 'Array
    123136      Designs'. Click on 'New ...'. In the 'Create array design'
    124       dialog, set the 'Name' (use the filename of the CDF file for
     137      dialog, set the 'Name' (use the file name of the CDF file for
    125138      convenience), tick the Affy chip tick box, choose a CDF file,
    126139      and optionally write a description. Click on next, and the new
    … …  
    131144      sufficient in most cases).
    132145
    133 4) Create an experiment, i.e., grouping .cel files into an experiment.
     146 4. Create an experiment, i.e., grouping .cel files into an
     147    experiment.
    134148
    135149    - Upload the .cel files into BASE.
    … …  
    146160      data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
    147161
    148 5) Select the experiment and create a new root bioassay set for it.
     162 5. Select the experiment and create a new root bioassay set for it.
    149163
    150164    - Locate the newly created experiment and click on 'Analyze'.
    151165
    152     - Click on 'New root bioassay set ...' and click 'Next' in the
    153       pop-up dialog. Select the 'Raw bioassays' to include in the new
    154       root bioassay set and type a name for the bioassay set. Click on
     166    - Click on 'New root bioassay set ...', select the algorithm you
     167      want to use in the import, and click 'Next' in the pop-up
     168      dialog. Select the 'Raw bioassays' to include in the new root
     169      bioassay set and type a name for the bioassay set. Click on
    155170      'Next' to start the plug-in.
    156171
    157 6) When the plug-in is finished the resulting expression values will
    158    be accessible in BASE.
     172 6. When the plug-in is finished the resulting expression values will
     173    be accessible in BASE.
     174
     175 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
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