Dear Laurent,

Thank you for your reply.

It' sworking fine with "PAe000002_mzXML_201106211454.tar.gz" this dataset
on my machine. But when I have used "PAe000030_mzXML_201104131929.tar.gz",
I got error. Here's the complete command and sessioninfo.

library(xcms)

files <- list.files("PAe000030",recursive=TRUE,full.names=TRUE)
files
 [1] "PAe000030/hui_serum10_full.mzXML"
 [2] "PAe000030/hui_serum16_full.mzXML"
 [3] "PAe000030/hui_serum17_full.mzXML"
 [4] "PAe000030/hui_serum18_full.mzXML"
 .
> xr<-xcmsRaw(files[1])
Warning message:
In `profStep<-`(`*tmp*`, value = 1) :
  MS1 scans empty. Skipping profile matrix calculation.
> xr<-xcmsRaw(files)
Error in file(con, "rb") : invalid 'description' argument
In addition: Warning message:
In if (!file.exists(filename)) return(FALSE) :
  the condition has length > 1 and only the first element will be used

> xr <- xcmsSet(files)
Error in x[1]:x[2] : NA/NaN argument


> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

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=C                LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] xcms_1.36.0        Biobase_2.20.1     BiocGenerics_0.6.0 mzR_1.6.2

[5] Rcpp_0.10.4

loaded via a namespace (and not attached):
[1] codetools_0.2-8

Kind Regards



On Tue, Aug 6, 2013 at 3:23 PM, Laurent Gatto <lg390@cam.ac.uk> wrote:

> Dear Reema,
>
> On 6 August 2013 10:22, Reema Singh <reema28sep@gmail.com> wrote:
> > Dear All,
> >
> > I am trying to import .mzXML files using XCMS package. I have tried it
> with
> > two different data set (
> > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030 ) and
> > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe0000<
> ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030>02).
> >  After extracting .mzXML files, when i tried to import them using XCMS, I
> > got this output.
> > *PAe000002*
> > files <- list.files("TEST", recursive=TRUE,full.names=TRUE)
> >> xr<-xcmsRaw(files[1])
> >> xr
> > An "xcmsRaw" object with 2070 mass spectra
> >
> > Time range: 120-5879.1 seconds (2-98 minutes)
> > Mass range: 400.0667-1399.9995 m/z
> > Intensity range: 1-465033000
> >
> > MSn data on  0  mass(es)
> > with  0  MSn spectra
> > Profile method: bin
> > Profile step: 1 m/z (1001 grid points from 400 to 1400 m/z)
> >
> > Memory usage: 34.4 MB
> >
> > *PAe000030*
> >
> >> files1 <- list.files("TEST1", recursive=TRUE,full.names=TRUE)
> >> xr1<-xcmsRaw(files1[1])
> > Warning message:
> > In `profStep<-`(`*tmp*`, value = 1) :
> >   MS1 scans empty. Skipping profile matrix calculation.
> >> xr1
> > An "xcmsRaw" object with 0 mass spectra
> >
> > MSn data on  0  mass(es)
> > with  0  MSn spectra
> > Profile method: bin
> > Profile step: no profile data
> >
> > Memory usage: 0.00481 MB
> >>
> >
> > Now My question is Why One dataset is successfulyy imported, whereas in
> the
> > same dataset got some warnings and datset with zero masses?.
> >
> > I would appreciate any help.
>
> First, we do not know exactly what files you are using for your test.
> Reading all of the PAe000030 mzXML files works well on my computer,
> indicating that it is likely not a mzXML issue as such.
>
> As the warning message suggests, the MS1 scans of that particular
> mzXML file are empty, which terminates the processing. Have you had
> more luck with another file from that experiment? You might want to
> check the offending mzXML file - it might indeed be valid yet 'empty'.
>
> Hope this helps,
>
> Laurent
>
> > Kind Regards
> >
> >
> > --
> > Reema Singh
> > PhD Scholar
> > Computational Biology and Bioinformatics
> > School of Computational and Integrative Sciences
> > Jawaharlal Nehru University
> > New Delhi-110067
> > INDIA
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> Laurent Gatto
> - http://proteome.sysbiol.cam.ac.uk/lgatto/
> Cambridge Centre for Proteomics
> - http://www.bio.cam.ac.uk/proteomics
> Using R/Bioconductor for proteomics data analysis
> - http://lgatto.github.io/RforProteomics/
>



-- 
Reema Singh
PhD Scholar
Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
INDIA

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