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 -- -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.