problem running XCMS

Skip to first unread message

Jul 20, 2015, 1:42:23 PM7/20/15

I'm new to metabolome and I'm having lots of difficulties. First, I could not install mzmatch, but it seems I finally made it (lol).
I tried the "combined" button, and show so many errors that I decided to do it step by step, to see where the problem was.
Then I used the "Convert RAW to mzXML files (and split polarity)" ideom button to convert my files and no warning message appeared, so it seemed all fine (the mzxml files created are 55kb more or less, is it ok?).
But when I tried using the "Run XCMS to pick peaks and convert to peakML files" ideom button, I received the following message.
How can I fix this error?
Thanks in advance,

> library (rJava)
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
Loading required package: Rcpp
Loading required package: xcms
Loading required package: mzR
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:rJava’:

    anyDuplicated, duplicated, sort, unique

The following object is masked from ‘package:stats’:


The following objects are masked from ‘package:base’:

    anyDuplicated, append,, as.vector, cbind, colnames,, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,, pmin,, Position, rank, rbind, Reduce,,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

Loading required package: ProtGenerics
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘xcms’

The following objects are masked from ‘package:Biobase’:

    phenoData, phenoData<-

> mzmatch.init (16000)
> rawfiles <- dir (full.names=TRUE,pattern="\\.mzXML*",recursive=TRUE)
> outputfiles <- paste(sub(".mzXML*","",rawfiles),".peakml",sep="")
> for (i in 1:length(rawfiles)){xset <- xcmsSet(rawfiles[i], method='centWave', ppm=2, peakwidth=c(5,100), snthresh=3, prefilter=c(3,1000), integrate=1, mzdiff=0,001, verbose.columns=TRUE, fitgauss=FALSE, nSlaves=1)
+ PeakML.xcms.write.SingleMeasurement (xset=xset,filename=outputfiles[i],ionisation="positive",addscans=2,writeRejected=FALSE,ApodisationFilter=TRUE)}
Error in seq.default(object@scanindex[scan] + 1, min(object@scanindex[scan +  : 
  'from' must be of length 1

Darren Creek

Jul 23, 2015, 6:30:14 PM7/23/15

Hi Adriana,
I have not seen this error before, but it looks like an issue with the file format.

Please specify which instrument you are using to collect this data, perhaps someone will have a solution. Otherwise also check the msconvert, xcms and mzmatch discussion boards.

All the best.

You received this message because you are subscribed to the Google Groups "Ideom" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
Visit this group at
For more options, visit
Reply all
Reply to author
0 new messages