Dear all,
I'm trying to run PSCBS on 126 matched pairs, but only 60 of them have run
without errors. The last error I got was when running callAB:
> deltaAB <- estimateDeltaAB(fit, scale=1)
> fit <- callAB(fit, delta=deltaAB, verbose=-10)
Calling segments of allelic balance from one-sided DH bootstrap confidence
intervals...
delta (offset adjusting for bias in DH): 0.181206399202347
alpha (CI quantile; significance level): 0.05
Error: all(segMean + tol >= range[, 1], na.rm = TRUE) is not TRUE
Calling segments of allelic balance from one-sided DH bootstrap confidence
intervals...done
> traceback()
17: base::stop(error)
16: throw.error(ex)
15: throw(ex)
14: value[[3L]](cond)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch({
fields <- dimnames(S)[[3]]
for (kk in seq(along = fields)) {
field <- fields[kk]
verbose && enter(verbose, sprintf("Field #%d ('%s') of %d",
kk, field, length(fields)))
Skk <- S[, , kk, drop = FALSE]
dim(Skk) <- dim(Skk)[-3]
stopifnot(is.matrix(Skk))
range <- Skk[, c(1, ncol(Skk)), drop = FALSE]
key <- sprintf("%sMean", field)
segMean <- segs[[key]]
verbose && printf(verbose, "mean: %g [%g,%g]\n", segMean,
range[1], range[2])
verbose && printf(verbose, "mean: %g, range: [%g,%g]\n",
segMean, range[1], range[2])
cfield <- sprintf("%sNbrOfLoci", ifelse(field == "tcn",
"tcn", "dh"))
counts <- segs[, cfield, drop = TRUE]
keep <- (counts > 1)
range <- range[keep, , drop = FALSE]
segMean <- segMean[keep]
stopifnot(all(range[, 2] + tol >= range[, 1], na.rm = TRUE))
stopifnot(all(segMean + tol >= range[, 1], na.rm = TRUE))
stopifnot(all(segMean - tol <= range[, 2], na.rm = TRUE))
verbose && exit(verbose)
}
}, error = function(ex) {
verbose && cat(verbose, "Tolerance (option
'PSCBS/sanityChecks/tolerance'): ",
tol)
verbose && print(verbose, segs)
throw(ex)
})
10: bootstrapTCNandDHByRegion.PairedPSCBS(fit, statsFcn = statsFcn,
..., verbose = less(verbose, 50))
9: bootstrapTCNandDHByRegion(fit, statsFcn = statsFcn, ..., verbose =
less(verbose,
50))
8: callAllelicBalanceByDH.PairedPSCBS(fit, ...)
7: callAllelicBalanceByDH(fit, ...)
6: callAB.PairedPSCBS(fit, delta = deltaAB)
5: callAB(fit, delta = deltaAB) at PSCSB_Manually.R#103
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("PSCSB_Manually.R")
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Hmisc_3.10-1 survival_2.36-14 DNAcopy_1.32.0
[4] PSCBS_0.30.0 aroma.affymetrix_2.6.0 affxparser_1.30.0
[7] aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.28.0
[10] aroma.core_2.8.0 matrixStats_0.6.2 R.rsp_0.8.2
[13] R.devices_2.1.3 R.cache_0.6.5 R.filesets_1.9.0
[16] R.utils_1.19.3 R.oo_1.11.7 R.methodsS3_1.4.2
loaded via a namespace (and not attached):
[1] cluster_1.14.3 digest_0.6.0 grid_2.15.1 lattice_0.20-10
[5] tools_2.15.1
Has anyone encountered a similar problem?
Thanks,
Oscar
Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Caldas Lab, Breast Cancer Functional
Genomics.
Cancer Research UK Cambridge Research Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE
England
Please note that my email address will be changing to:
oscar.ru...@cruk.cam.ac.uk
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