[Bioc-devel] xcms adjustRtime-obiwarp Error
Rainer Johannes
Johannes.Rainer at eurac.edu
Thu Jul 27 13:37:05 CEST 2017
Dear Riccardo,
I will look closer into this. In the meantime it might help if you try a different binSize in the ObiwarpParam. Also, could you please add an issue with this error on https://github.com/sneumann/xcms ? I can then track and relate all changes to the issue.
thanks, jo
On 27 Jul 2017, at 12:56, Riccardo Romoli <riccardo.romoli at unifi.it<mailto:riccardo.romoli at unifi.it>> wrote:
Dear xcms devel,
running the latest stable xcms version I get the following error:
> xod <- adjustRtime(xod, param = ObiwarpParam())
Sample number 3 used as center sample.
Aligning pl55_06h_01.mzXML against pl55_03h_01.mzXML ...
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5
first error: Dimensions of profile matrices of files pl55_03h_01.mzXML and pl4_01.mzXML do not match!
This is the traceback:
> traceback()
9: stop(.error_bplist(res))
8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
6: bplapply(objL, function(z, cntr, cntrPr, parms) {
message("Aligning ", basename(fileNames(z)), " against ",
basename(fileNames(cntr)), " ... ", appendLF = FALSE)
suppressMessages(curP <- profMat(z, method = "bin", step = binSize(parms),
returnBreaks = TRUE)[[1]])
scantime1 <- unname(rtime(cntr))
scantime2 <- unname(rtime(z))
mstdiff <- median(c(diff(scantime1), diff(scantime2)))
mst1 <- which(diff(scantime1) > 5 * mstdiff)[1]
if (!is.na(mst1)) {
scantime1 <- scantime1[seq_len((mst1 - 1))]
message("Found gaps in scan times of the center sample: cut ",
"scantime-vector at ", scantime1[mst1], " seconds.")
}
mst2 <- which(diff(scantime2) > 5 * mstdiff)[1]
if (!is.na(mst2)) {
scantime2 <- scantime2[seq_len((mst2 - 1))]
message("Found gaps in scan time of file ", basename(fileNames(z)),
": cut scantime-vector at ", scantime2[mst2], " seconds.")
}
rtmaxdiff <- abs(diff(c(scantime1[length(scantime1)], scantime2[length(scantime2)])))
if (rtmaxdiff > (5 * mstdiff)) {
rtmax <- min(scantime1[length(scantime1)], scantime2[length(scantime2)])
scantime1 <- scantime1[scantime1 <= rtmax]
scantime2 <- scantime2[scantime2 <= rtmax]
}
valscantime1 <- length(scantime1)
valscantime2 <- length(scantime2)
if (ncol(cntrPr$profMat) > valscantime1) {
cntrPr$profMat <- cntrPr$profMat[, -c((valscantime1 +
1):ncol(cntrPr$profMat))]
}
if (ncol(curP$profMat) > valscantime2) {
curP$profMat <- curP$profMat[, -c((valscantime2 + 1):ncol(curP$profMat))]
}
mzr1 <- c(cntrPr$breaks[1], cntrPr$breaks[length(cntrPr$breaks) -
1])
mzr2 <- c(curP$breaks[1], curP$breaks[length(curP$breaks) -
1])
mzmin <- min(c(mzr1[1], mzr2[1]))
mzmax <- max(c(mzr1[2], mzr2[2]))
mzs <- seq(mzmin, mzmax, by = binSize(parms))
if (mzmin < mzr1[1]) {
tmp <- matrix(0, (length(seq(mzmin, mzr1[1], binSize(parms))) -
1), ncol = ncol(cntrPr$profMat))
cntrPr$profMat <- rbind(tmp, cntrPr$profMat)
}
if (mzmax > mzr1[2]) {
tmp <- matrix(0, (length(seq(mzr1[2], mzmax, binSize(parms))) -
1), ncol = ncol(cntrPr$profMat))
cntrPr$profMat <- rbind(cntrPr$profMat, tmp)
}
if (mzmin < mzr2[1]) {
tmp <- matrix(0, (length(seq(mzmin, mzr2[1], binSize(parms))) -
1), ncol = ncol(curP$profMat))
curP$profMat <- rbind(tmp, curP$profMat)
}
if (mzmax > mzr2[2]) {
tmp <- matrix(0, (length(seq(mzr2[2], mzmax, binSize(parms))) -
1), ncol = ncol(curP$profMat))
curP$profMat <- rbind(curP$profMat, tmp)
}
mzvals <- length(mzs)
cntrVals <- length(cntrPr$profMat)
curVals <- length(curP$profMat)
if ((mzvals * valscantime1) != cntrVals | (mzvals * valscantime2) !=
curVals | cntrVals != curVals)
stop("Dimensions of profile matrices of files ", basename(fileNames(cntr)),
" and ", basename(fileNames(z)), " do not match!")
rtadj <- .Call("R_set_from_xcms", valscantime1, scantime1,
mzvals, mzs, cntrPr$profMat, valscantime2, scantime2,
mzvals, mzs, curP$profMat, response(parms), distFun(parms),
gapInit(parms), gapExtend(parms), factorDiag(parms),
factorGap(parms), as.numeric(localAlignment(parms)),
initPenalty(parms))
if (length(rtime(z)) > valscantime2) {
rtadj <- c(rtadj, rtime(z)[(valscantime2 + 1):length(rtime(z))])
warning(basename(fileNames(z)), " :could only align up to a ",
"retention time of ", rtime(z)[valscantime2], " seconds. ",
"After that raw retention times are reported.")
}
message("OK")
return(rtadj)
}, cntr = centerObject, cntrPr = profCtr, parms = param)
5: bplapply(objL, function(z, cntr, cntrPr, parms) {
message("Aligning ", basename(fileNames(z)), " against ",
basename(fileNames(cntr)), " ... ", appendLF = FALSE)
suppressMessages(curP <- profMat(z, method = "bin", step = binSize(parms),
returnBreaks = TRUE)[[1]])
scantime1 <- unname(rtime(cntr))
scantime2 <- unname(rtime(z))
mstdiff <- median(c(diff(scantime1), diff(scantime2)))
mst1 <- which(diff(scantime1) > 5 * mstdiff)[1]
if (!is.na(mst1)) {
scantime1 <- scantime1[seq_len((mst1 - 1))]
message("Found gaps in scan times of the center sample: cut ",
"scantime-vector at ", scantime1[mst1], " seconds.")
}
mst2 <- which(diff(scantime2) > 5 * mstdiff)[1]
if (!is.na(mst2)) {
scantime2 <- scantime2[seq_len((mst2 - 1))]
message("Found gaps in scan time of file ", basename(fileNames(z)),
": cut scantime-vector at ", scantime2[mst2], " seconds.")
}
rtmaxdiff <- abs(diff(c(scantime1[length(scantime1)], scantime2[length(scantime2)])))
if (rtmaxdiff > (5 * mstdiff)) {
rtmax <- min(scantime1[length(scantime1)], scantime2[length(scantime2)])
scantime1 <- scantime1[scantime1 <= rtmax]
scantime2 <- scantime2[scantime2 <= rtmax]
}
valscantime1 <- length(scantime1)
valscantime2 <- length(scantime2)
if (ncol(cntrPr$profMat) > valscantime1) {
cntrPr$profMat <- cntrPr$profMat[, -c((valscantime1 +
1):ncol(cntrPr$profMat))]
}
if (ncol(curP$profMat) > valscantime2) {
curP$profMat <- curP$profMat[, -c((valscantime2 + 1):ncol(curP$profMat))]
}
mzr1 <- c(cntrPr$breaks[1], cntrPr$breaks[length(cntrPr$breaks) -
1])
mzr2 <- c(curP$breaks[1], curP$breaks[length(curP$breaks) -
1])
mzmin <- min(c(mzr1[1], mzr2[1]))
mzmax <- max(c(mzr1[2], mzr2[2]))
mzs <- seq(mzmin, mzmax, by = binSize(parms))
if (mzmin < mzr1[1]) {
tmp <- matrix(0, (length(seq(mzmin, mzr1[1], binSize(parms))) -
1), ncol = ncol(cntrPr$profMat))
cntrPr$profMat <- rbind(tmp, cntrPr$profMat)
}
if (mzmax > mzr1[2]) {
tmp <- matrix(0, (length(seq(mzr1[2], mzmax, binSize(parms))) -
1), ncol = ncol(cntrPr$profMat))
cntrPr$profMat <- rbind(cntrPr$profMat, tmp)
}
if (mzmin < mzr2[1]) {
tmp <- matrix(0, (length(seq(mzmin, mzr2[1], binSize(parms))) -
1), ncol = ncol(curP$profMat))
curP$profMat <- rbind(tmp, curP$profMat)
}
if (mzmax > mzr2[2]) {
tmp <- matrix(0, (length(seq(mzr2[2], mzmax, binSize(parms))) -
1), ncol = ncol(curP$profMat))
curP$profMat <- rbind(curP$profMat, tmp)
}
mzvals <- length(mzs)
cntrVals <- length(cntrPr$profMat)
curVals <- length(curP$profMat)
if ((mzvals * valscantime1) != cntrVals | (mzvals * valscantime2) !=
curVals | cntrVals != curVals)
stop("Dimensions of profile matrices of files ", basename(fileNames(cntr)),
" and ", basename(fileNames(z)), " do not match!")
rtadj <- .Call("R_set_from_xcms", valscantime1, scantime1,
mzvals, mzs, cntrPr$profMat, valscantime2, scantime2,
mzvals, mzs, curP$profMat, response(parms), distFun(parms),
gapInit(parms), gapExtend(parms), factorDiag(parms),
factorGap(parms), as.numeric(localAlignment(parms)),
initPenalty(parms))
if (length(rtime(z)) > valscantime2) {
rtadj <- c(rtadj, rtime(z)[(valscantime2 + 1):length(rtime(z))])
warning(basename(fileNames(z)), " :could only align up to a ",
"retention time of ", rtime(z)[valscantime2], " seconds. ",
"After that raw retention times are reported.")
}
message("OK")
return(rtadj)
}, cntr = centerObject, cntrPr = profCtr, parms = param)
4: .obiwarp(as(object, "OnDiskMSnExp"), param = param)
3: .local(object, param, ...)
2: adjustRtime(xod, param = ObiwarpParam())
1: adjustRtime(xod, param = ObiwarpParam())
>
These are the sessionInfo():
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grDevices datasets parallel stats graphics utils methods
[8] base
other attached packages:
[1] RColorBrewer_1.1-2 CAMERA_1.32.0 xcms_1.52.0
[4] MSnbase_2.2.0 ProtGenerics_1.8.0 mzR_2.10.0
[7] Rcpp_0.12.12 BiocParallel_1.10.1 Biobase_2.36.2
[10] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] splines_3.4.1 lattice_0.20-35 colorspace_1.3-2
[4] htmltools_0.3.6 stats4_3.4.1 base64enc_0.1-3
[7] vsn_3.44.0 survival_2.41-3 XML_3.98-1.9
[10] RBGL_1.52.0 rlang_0.1.1 foreign_0.8-69
[13] affy_1.54.0 affyio_1.46.0 foreach_1.4.3
[16] plyr_1.8.4 stringr_1.2.0 mzID_1.14.0
[19] zlibbioc_1.22.0 munsell_0.4.3 pcaMethods_1.68.0
[22] gtable_0.2.0 htmlwidgets_0.9 codetools_0.2-15
[25] knitr_1.16 latticeExtra_0.6-28 IRanges_2.10.2
[28] doParallel_1.0.10 BiocInstaller_1.26.0 MassSpecWavelet_1.42.0
[31] preprocessCore_1.38.1 htmlTable_1.9 acepack_1.4.1
[34] backports_1.1.0 checkmate_1.8.3 scales_0.4.1
[37] limma_3.32.4 S4Vectors_0.14.3 Hmisc_4.0-3
[40] graph_1.54.0 gridExtra_2.2.1 RANN_2.5.1
[43] impute_1.50.1 ggplot2_2.2.1 digest_0.6.12
[46] stringi_1.1.5 grid_3.4.1 tools_3.4.1
[49] magrittr_1.5 lazyeval_0.2.0 tibble_1.3.3
[52] Formula_1.2-2 cluster_2.0.6 pkgconfig_2.0.1
[55] MASS_7.3-47 Matrix_1.2-10 data.table_1.10.4
[58] iterators_1.0.8 MALDIquant_1.16.2 rpart_4.1-11
[61] igraph_1.1.2 multtest_2.32.0 nnet_7.3-12
[64] compiler_3.4.1
>
Hope you can help me and fix the issue.
All the best,
Riccardo
--
Riccardo Romoli, PhD
Mass Spectrometry Centre - CISM
University of Florence
Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
Phone: +39 055 4573783/2
email: riccardo.romoli at unifi.it<mailto:riccardo.romoli at unifi.it>
web site: www.cism.unifi.it<http://www.cism.unifi.it>
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