Thanks Henrik,
You are right. The sample is really noisy.
On Wednesday, February 18, 2015 at 11:23:13 PM UTC+2, Henrik Bengtsson
wrote:
>
> I'll try to catch up with a few questions; comments below.
>
> On Mon, Feb 9, 2015 at 3:52 AM, Chengyu Liu <chengyu...@gmail.com
> <javascript:>> 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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