inst/testScripts/system/chipTypes/Mapping250K_Nsp/31.doASCRMAv2,TumorNormalPair.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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# Allele-specific CRMAv2
#
# Author: Henrik Bengtsson
# Created on: 2011-11-11
# Last updated: 2016-01-06
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library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)


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# Setup
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dataSet <- "GSE34754"
chipType <- "Mapping250K_Nsp"

csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)


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# Extract a single tumor-normal pair
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# Extract tumor-normal pair
pair <- c(T="GSM854620", N="GSM854615")
csR <- csR[indexOf(csR, pair)]
print(csR)


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# AS-CRMAv2
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dsNList <- doASCRMAv2(csR, verbose=verbose)
print(dsNList)