I wanted to reproduce the results of FIRMA paper for the tissue sample
data set (exon array:HuEx-1_0-st-v2) . I used the ensebl cdf,
HuEx-1_0-st-v2,U-Ensembl47,G-Affy which I think is the one the authors
used. Here is the exact code that I used:
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
# Getting annotation data files
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="U-Ensembl47,G-
Affy")
# Defining CEL set
cs <- AffymetrixCelSet$byName("coloncancer", cdf=cdf)
#Background Adjustment and Normalization
bc <- RmaBackgroundCorrection(cs, tag="ensemblcancer")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
#Summarization
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
CesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(CesTr,units=NULL,addNames=TRUE)
#Alternative Splicing Analysis (FIRMA)
firma <- FirmaModel(plmTr)
fit(firma, verbose=verbose)
fs <- getFirmaScores(firma)
firma <- extractDataFrame(fs,units=NULL,addNames=TRUE)
rownames(firma) = firma$groupName
I am getting some FIRMA values as high as 1568 ( for UNR: 2429323). Is
that even feasible ?
Gaurav Bhatti
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