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XCMS / Re: Weird errors with xcmsSet
I don't understand how repeating the same step twice can lead to different results.
Did someone encounter the same problem?
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> path<-"Files/"
> files<-list.files(path, recursive=TRUE, full.names=TRUE)
> files
[1] "Files//Ctrl/20141031_IPMS33-IP Flag C Ctrl.mzXML"
[2] "Files//PRMT5/20141031_IPMS36-IP Flag C PRMT5 0.mzXML"
> xset<-xcmsSet(files)
400:1072 450:2307 500:3642 550:4917 600:6269 650:7556 700:8729 750:9929 800:10959 850:11925 900:12762 950:13681 1000:14371 1050:14913 1100:15469 1150:16017 1200:16366 1250:16661
Error in rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans]) :
unexpected end of peak list
> traceback()
10: .Call("RampRSIPeaks", as.integer(rampid), seqNum, peaksCount,
PACKAGE = "mzR")
9: rampSIPeaks(rampid, scans, scanHeaders$peaksCount[scans])
8: mzR:::rampRawData(object@rampid)
7: .local(object, ...)
6: loadRaw(object@filepath, includeMSn)
5: loadRaw(object@filepath, includeMSn)
4: xcmsRaw(arg$file, profmethod = params$profmethod, profparam = params$profparam,
profstep = 0, includeMSn = params$includeMSn, mslevel = params$mslevel,
scanrange = params$scanrange)
3: FUN(X[[2L]], ...)
2: lapply(argList, findPeaksPar)
1: xcmsSet(files)
> xset<-xcmsSet(files)
Error in seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * :
'by' argument is much too small
> traceback()
10: stop("'by' argument is much too small")
9: seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *
step, by = step)
8: seq(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * step,
by = step)
7: .local(object, ...)
6: findPeaks.matchedFilter(object = <S4 object of class "xcmsRaw">)
5: findPeaks.matchedFilter(object = <S4 object of class "xcmsRaw">)
4: do.call(method, params)
3: FUN(X[[1L]], ...)
2: lapply(argList, findPeaksPar)
1: xcmsSet(files)
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] grDevices datasets parallel stats graphics stats4 utils methods base
other attached packages:
[1] xcms_1.42.0 mzR_2.0.0 Rcpp_0.11.4 AnnotationDbi_1.28.1 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0 Biobase_2.26.0 BiocGenerics_0.12.1 RSQLite_1.0.0 DBI_0.3.1
loaded via a namespace (and not attached):
[1] clusterProfiler_2.0.0 codetools_0.2-10 colorspace_1.2-4 digest_0.6.8 DO.db_2.8.0 DOSE_2.4.0 ggplot2_1.0.0 GO.db_3.0.0 GOSemSim_1.24.1 grid_3.1.2
[11] gtable_0.1.2 igraph_0.7.1 KEGG.db_3.0.0 MASS_7.3-37 munsell_0.4.2 plyr_1.8.1 proto_0.3-10 qvalue_1.40.0 reshape2_1.4.1 scales_0.2.4
[21] stringr_0.6.2 tools_3.1.2