inst/testScripts/addons/chipTypes/Mapping250K_Nsp/21.doASCRMAv2,CalMaTe.R

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

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# Allele-specific CRMAv2 and CalMaTe
#
# Author: Henrik Bengtsson
# Created on: 2012-06-15
# Last updated: 2016-01-06
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library("aroma.affymetrix")
library("calmate")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)


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# Setup
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dataSet <- "GSE12702"
chipType <- "Mapping250K_Nsp"

csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
csR <- csR[1:12]
print(csR)


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


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# CalMaTe
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cmt <- CalMaTeCalibration(dsList)
print(cmt)

dsCList <- process(cmt, verbose=verbose)
print(dsCList)