inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/21.doFIRMA,extras.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-3, timestamp=TRUE)


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# Setup data set
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dataSet <- "Affymetrix-HeartBrain"
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
print(cdf)

# Setup CEL set using the core CDF.
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)


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# Process only cerebellum and heart
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types <- c("cerebellum", "heart")
csR <- csR[indexOf(csR, patterns=types)]

setFullName(csR, sprintf("%s,%s", dataSet, paste(types, collapse="+")))
print(csR)


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# FIRMA
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res <- doFIRMA(csR, drop=FALSE, verbose=verbose)
print(res)


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# PLMs
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plmList <- list(
  merge   = res$plm,                               # all exons together
  noMerge = ExonRmaPlm(res$csN, mergeGroups=FALSE) # each exon separately
)
print(plmList)

# Fit the per-exon PLM
fit(plmList$noMerge, verbose=verbose)


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# PLM residuals (also calculated by FIRMA)
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resList <- lapply(plmList, FUN=calculateResidualSet, verbose=verbose)
print(resList)


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# PLM weights
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weightList <- lapply(plmList, FUN=calculateWeights, verbose=verbose)
print(weightList)