inst/testScripts/system/chipTypes/Mapping50K_Hind240/11.justSNPRMA.R

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

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


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# Setup
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dataSet <- "HapMap,CEU,testset"
chipType <- "Mapping50K_Hind240"

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


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# SNPRMA according to aroma.affymetrix
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eSet <- justSNPRMA(csR, normalizeToHapmap=TRUE, verbose=verbose)
print(eSet)