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:

verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
# Getting annotation data files
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="U-Ensembl47,G-
# Defining CEL set
cs <- AffymetrixCelSet$byName("coloncancer", cdf=cdf)
#Background Adjustment and Normalization
bc <- RmaBackgroundCorrection(cs, tag="ensemblcancer")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
CesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(CesTr,units=NULL,addNames=TRUE)
#Alternative Splicing Analysis (FIRMA)
firma <- FirmaModel(plmTr)
fit(firma, verbose=verbose)
fs <- getFirmaScores(firma)
firma <- extractDataFrame(fs,units=NULL,addNames=TRUE)
rownames(firma) = firma$groupName
I am getting some FIRMA values as high as 1568 ( for UNR: 2429323). Is
that even feasible ?

Gaurav Bhatti

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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