inst/testScripts/system/chipTypes/Mapping10K_Xba142/22.doASCRMAv2,TotalFreqB.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)

csR <- AffymetrixCelSet$byName("GSE8605", chipType="Mapping10K_Xba142")
print(csR)

cesN <- doASCRMAv2(csR, arrays=1:6, drop=FALSE, verbose=verbose)$cesN
print(cesN)


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# Export to (total,fracB) ASB files
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theta <- getAromaUnitTotalCnBinarySet(cesN, verbose=verbose)
print(theta)

fracB <- getAromaUnitFracBCnBinarySet(cesN, verbose=verbose)
print(fracB)


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# Calculate average theta across arrays
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thetaR <- calculateAverageColumnAcrossFiles(theta, verbose=verbose)
str(thetaR)