Hi there,
I'm new to the whole xcms package, but it looks like a powerful tool to analyse MS data.
I tried to mess around with the programm a bit, to see what kind of results I could get from it. I used two .wiff files that I converted to .mzXML files using ProteoWizard.
I put the filenames in a vector with :
> 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"
Now when I try to use the xcmsSet command, I get all kinds of weird errors, and they are not the same from time to time. Sometimes the first file would get processed, as evidenced by the apparition of the following :
> 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)
Sometimes it simply won't start :
> 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)
And sometimes, R crashes. I managed to get both files processed once, but the grouping step would fail as well. Could you guys help me out on this one?
Here are my infos :
> 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
Topic: Weird errors with xcmsSet