On 6 August 2013 14:12, Reema Singh <reema28sep at="" gmail.com=""> wrote: > 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. Investigating the content of the files sheds some light on the source of the error. None of the 64 files has any MS1 spectra - they only contain MS2 spectra. The observed result seems thus to be correct. >> 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 Based on ?xcmsRaw, this is not supposed to work - xcmsRaw that a single file as input, as stated by the warning. >> xr <- xcmsSet(files) > Error in x[1]:x[2] : NA/NaN argument Same explanation as above, I assume. Hope this helps. Best wishes, Laurent >> 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 at="" cam.ac.uk=""> wrote: >> >> Dear Reema, >> >> On 6 August 2013 10:22, Reema Singh <reema28sep at="" 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<ft p:="" 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 at 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 -- 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/