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TITLE: README
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Author: Henrik Bengtsson
Created on: 2011-03-09
Last updated on: 2011-03-09


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INTRODUCTION
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SCRIPTS
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DATA SETS
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The following data sets are used in these scripts.  Some are
publicly available, whereas some requires certain prior approvals
before the resource allows you to download the data.


DATA SET: GEO GSE12702 Affymetrix data set

annotationData/
  chipTypes/
    Mapping250K_Nsp/
      Mapping250K_Nsp.cdf
      Mapping250K_Nsp,HB20080710.acs
      Mapping250K_Nsp,na31,HB20101007.ufl
      Mapping250K_Nsp,na31,HB20101007.ugp

rawData/
  GSE12702/
    Mapping250K_Nsp/
      GSM318728.CEL [File #1]
      ...
      GSM318767.CEL [File #40]



DATA SET: TCGA Affymetrix data set

annotationData/
  chipTypes/
    GenomeWideSNP_6/
      GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp

totalAndFracBData/
  broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0,ASCRMAv2/
    GenomeWideSNP_6/
      .average-signals-median-mad,<hashcode>.asb
      <sampleName>,total.asb
      <sampleName>,fracB.asb
  broad.mit.edu_OV.Genome_Wide_SNP_6.12.6.0,ASCRMAv2,CMTN/
    GenomeWideSNP_6/
      <sampleName>,total.asb
      <sampleName>,fracB.asb

Availability: This data set is available from the TCGA portal.  It is only available for people with access to the "protected" TCGA data.




DATA SET: TCGA Illumina data set

annotationData/
  chipTypes/
    Human1M-Duo/
      Human1M-Duo,HB20090419.ugp

totalAndFracBData/
  hudsonalpha.org_OV.Human1MDuo.1.1.0,XY/
    Human1M-Duo/
      .average-signals-median-mad,<hashcode>.asb
      <sampleName>,total.asb
      <sampleName>,fracB.asb
  hudsonalpha.org_OV.Human1MDuo.1.1.0,XY,CMTN/
    Human1M-Duo/
      <sampleName>,total.asb
      <sampleName>,fracB.asb

Availability: This data set is available from the TCGA portal.  It is only available for people with access to the "protected" TCGA data.
