inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/81.fnt.R

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

library("aroma.affymetrix")

verbose <- Verbose(threshold=-4, timestamp=TRUE)

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# A tuple
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dataSet <- "HapMap,CEU,testset"
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")

dsList <- lapply(chipTypes, FUN=function(chipType) {
  AffymetrixCelSet$byName(dataSet, chipType=chipType)
})
print(dsList)
dsTuple <- AffymetrixCelSetTuple(dsList)
dsTuple <- GenericDataFileSetList(dsList)
print(dsTuple)
print(getNames(dsTuple));  # HMM... == NULL?!?


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# Same tuple with fullname translators
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for (ds in getSets(dsTuple)) {
  fnts <- getAromaFullNameTranslatorSet(ds)
  appendFullNamesTranslator(ds, fnts)
}
print(dsTuple)
print(getNames(dsTuple))


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Attributes
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ds <- dsList[[1]]
n23 <- sapply(ds, getAttribute, "n23")
n24 <- sapply(ds, getAttribute, "n24")
isFemale <- (n23 == 2 & n24 == 0)
dsXX <- ds[isFemale]
print(dsXX)