problem running XCMS

[drikca...@gmail.com]

Hello,

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,

Adriana

setwd("D:/DIFT_Pos_Jun")

> 

> 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’:

    xtabs

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

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,

    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,

    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,

    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,

    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)

C:/R/R-3.2.1/library/mzmatch.R/java/mzmatch.jar 

> 

> 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]

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.
Darren

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