Hi all,
I have a batch of 107 mice exon arrays for which I computed FIRMA
scores and I got many NaN, Inf and 0 values which disable further
analysis based on log FIRMA values for some probesets. I was wondering
if this is a known issue or I am the only one to get these results.
Here is the code I use to get the FIRMA scores:
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "MoEx-1_0-st-v1"
cdf <- AffymetrixCdfFile$byChipType(chipType,
tags="fullR1,A20080718,MR")
cs <- AffymetrixCelSet$byName("mice2010", cdf=cdf)
bc <- RmaBackgroundCorrection(cs, tag="fullR1,A20080718,MR")
csBC <- process(bc,verbose=verbose,ram=500)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose,ram=500)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose,ram=500)
firma <- FirmaModel(plmTr)
fit(firma, verbose=verbose,ram=500)
fs <- getFirmaScores(firma)
myres2=extractDataFrame(fs,addNames=FALSE)
myres=as.matrix(myres2[,-(1:3)])
Here is the counts of NaN Inf and 0 values:
> dim(myres)
[1] 1190297 107
> sum(is.nan(myres))
[1] 431210
> sum(is.infinite(myres),na.rm=TRUE)
[1] 855
> sum(myres==0,na.rm=TRUE)
[1] 214
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7
affxparser_1.20.0
[4] R.huge_0.2.0 aroma.core_1.5.0
aroma.light_1.16.0
[7] matrixStats_0.2.1 R.rsp_0.3.6
R.cache_0.3.0
[10] R.filesets_0.8.1 digest_0.4.2
R.utils_1.4.0
[13] R.oo_1.7.2 R.methodsS3_1.2.0
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