I'll try to catch up with a few questions; comments below.
On Mon, Feb 9, 2015 at 3:52 AM, Chengyu Liu <chengyu.liu...@gmail.com> wrote:
> 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 ?
This is a sanity check kicking in preventing a likely error in
data/annotation from propagating further in your analysis. As genome
types are called from the normal BAFs, i.e. betaN = d[, 5] in your
case. Have a look at those BAF signals, e.g. plotDensity(betaN) to
see if they're showing the three expected BAF modes near 0%, 50% and
100%. If your data is extremely noisy genotype calling will fail.
Internally, segmentByPairedPSCBS() uses:
muN <- aroma.light::callNaiveGenotypes(betaN, censorAt=c(0,1))
so you can look at the calls made that way too.
Hope this helps
/Henrik
>
>
> Br,
> Chengyu
>
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