Hi,
I am doing allele-specific analysis using PSCBS package. I have paired
tumor-normal matched samples.
For one of the samples, i got an error which is like
at #06. lapply(names.T[8:length(names.T)], function(x) {
print(x)
y <- grep(x, names(df))
if (length(y) != 3) {
stop("Length of y is not 3")
}
d <- dropSegmentationOutliers(y = df[, y[1]], chromosome =
df[,
1], x = df[, 2])
d <- data.frame(chromosome = df[, 1], x = df[, 2], CT = d,
betaT = df[, y[2]], betaN = df[, y[3]])
fit <- segmentByPairedPSCBS(CT = d[, 3], betaT = d[, 4],
betaN = d[, 5], chromosome = d$chromosome, x = d$x)
segs <- getSegments(fit)
pairName <- x
chrTag <- sprintf("Chr%s",
seqToHumanReadable(getChromosomes(fit)))
toPNG(pairName, tags = c(chrTag, "PairedPSCBS"), width = 840,
aspectRatio = 0.6, {
plotTracks(fit)
})
ret <- data.frame(sample = x, segs)
return(ret)
})
- lapply() is in environment 'base'
- originating from 'cytoscanHD.processing.R'
at #05. aroma.affy.snp.preprocessing(path =
"/storageBig/storageBig1/czliu/input/azhar/aroma/",
chipType = "CytoScanHD_Array", dataSet = "dataset1",
combineAlleles = FALSE,
paired = TRUE, verbose = FALSE, PSCNA = FALSE, na.rm = TRUE)
- aroma.affy.snp.preprocessing() is in environment 'R_GlobalEnv'
- originating from 'cytoscanHD.processing.R'
at #04. eval(expr, envir, enclos)
- eval() is local of the calling function
at #03. eval(ei, envir)
- eval() is in environment 'base'
at #02. withVisible(eval(ei, envir))
- withVisible() is in environment 'base'
at #01. source("cytoscanHD.processing.R")
- source() is in environment 'base'
Error: All genotypes ('muN') called from the normal allele B fractions
('betaN') are NAs: 2819494 (100%) out of 2819494
In addition: There were 30 warnings (use warnings() to see them)
It seems all BAF values were NA. Why does it happen ? Is there something
wrong with the sample ?
Br,
Chengyu
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