Changeset 276


Ignore:
Timestamp:
May 21, 2007, 7:44:04 PM (16 years ago)
Author:
Peter Johansson
Message:

updated README for affy package refs #45

File:
1 edited

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

    r275 r276  
    2626----------------------------------------------------------------------
    2727
    28 = About se.lu.thep.affymetrix package ===
     28= About se.lu.thep.affymetrix package =
    2929
    3030Send comments, suggestion, complaints, or questions about this
     
    4141
    4242
    43 What is RMAExpress plug-in for BASE?
     43What is RMAExpress and Plier plug-ins for BASE?
    4444
    45 Currently, this is a tool needed to make use of Affymetrix data in
    46 BASE. Affymetrix data can be imported into BASE as files, but if one
    47 wants to perform clustering and other analysis available in BASE, the
    48 data in these files have to be extracted and imported into BASE. There
    49 may (and probably will) be other ways to analyze Affymetrix data in
    50 BASE in the future.
     45RMAExpress and Plier are two similar plug-ins needed to make use of
     46Affymetrix data in BASE. Affymetrix data can be imported into BASE as
     47files, but if one wants to perform clustering and other analysis
     48available in BASE, the data in these files have to be extracted and
     49imported into BASE.
    5150
    52 This plug-in do not implement the RMA method itself but rather relies
    53 on RMAExpressConsole available in the RMAExpress package available at
    54 http://rmaexpress.bmbolstad.com/. The RMA algorithm is published in
    55 scientific journals, for more information please refer to the
    56 RMAExpress web site. In short RMA is the Robust Multichip Average. It
    57 consists of three steps: a background adjustment, quantile
    58 normalization, and finally a summarization.
     51These plug-ins do not implement the RMA method and Plier method,
     52respectively, but rather relies on third-party binary packages.
    5953
     54The RMAExpress plug-in relies on RMAExpressConsole available in the
     55RMAExpress package available at http://rmaexpress.bmbolstad.com/. The
     56RMA algorithm is published in scientific journals, for more
     57information please refer to the RMAExpress web site. In short RMA is
     58the Robust Multichip Average. It consists of three steps: a background
     59adjustment, quantile normalization, and finally a summarization.
    6060
    61 What is required to use the RMAExpress plug-in for BASE? The "BASE
     61The Plier plug-in relies on `apt-probeset-summarize` included in
     62Affymetrix Power Tools (APT) available at
     63http://www.affymetrix.com/support/developer/powertools/index.affx.
     64`apt-probeset-summarize` provides several methods (see Affymetrix home
     65page). Here we use the method given with option flag `--option
     66plier-mm`.
     67
     68What is required to use the these plug-ins for BASE? The "BASE
    6269getting started document" may also be helpful,
    6370http://base.thep.lu.se/chrome/site/doc/user/getting_started.html
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