Hi,
sorry for the delay - I've been "off the grid" since two weeks.
On Thu, Jan 24, 2013 at 4:09 AM, Oscar Rueda <oscar.ru...@cruk.cam.ac.uk> wrote:
> 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
That is an internal "sanity" check part of a bootstrap estimation that
fails. The code has a lot of such assertion tests to validate that
intermediate and final estimates are sound and valid. It may be that
this one is a bit too conservative.
To troubleshoot, with a sample that fails, first confirm that you get
the same error by calling the internal bootstrap estimator explicitly:
fitB <- bootstrapTCNandDHByRegion(fit, verbose=-10);
It should, but if not, try another sample (aka 'fit'). Then, look for
the verbose output that looks something like:
Field #2 ('dh') of 4...
mean: 0.6645 [0.648152,0.112718]
mean: 0.1282 [0.648152,0.112718]
mean: 0.3038 [0.648152,0.112718]
mean: 0.6645, range: [0.648152,0.112718]
mean: 0.1282, range: [0.648152,0.112718]
mean: 0.3038, range: [0.648152,0.112718]
...
Tolerance (option 'PSCBS/sanityChecks/tolerance'): 5e-04
and some segment table followed by the error message. What do you get?
Also, when you find a sample that gives the error, save it
saveObject(fit, "faultySample.Rbin")
and make the file available to me for download (<20Mb can be emailed)
and I can have a look at it.
/Henrik
>
>> 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
>
>
>
> --
> 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.
>
>
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