Nothing
library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-3, timestamp=TRUE)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "Affymetrix-HeartBrain"
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
print(cdf)
# Setup CEL set using the core CDF.
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Process only cerebellum and heart
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
types <- c("cerebellum", "heart")
csR <- csR[indexOf(csR, patterns=types)]
setFullName(csR, sprintf("%s,%s", dataSet, paste(types, collapse="+")))
print(csR)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# FIRMA
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
res <- doFIRMA(csR, drop=FALSE, verbose=verbose)
print(res)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# PLMs
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
plmList <- list(
merge = res$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)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# PLM residuals (also calculated by FIRMA)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
resList <- lapply(plmList, FUN=calculateResidualSet, verbose=verbose)
print(resList)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# PLM weights
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
weightList <- lapply(plmList, FUN=calculateWeights, verbose=verbose)
print(weightList)
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