Question: XCMS query regarding mzXML
0
gravatar for Reema Singh
6.2 years ago by
Reema Singh570
Reema Singh570 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: f="" tp.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. 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]]
xcms • 1.4k views
ADD COMMENTlink modified 6.2 years ago by Laurent Gatto1.2k • written 6.2 years ago by Reema Singh570
Answer: XCMS query regarding mzXML
0
gravatar for Laurent Gatto
6.2 years ago by
Laurent Gatto1.2k
Belgium
Laurent Gatto1.2k 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<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 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/
ADD COMMENTlink written 6.2 years ago by Laurent Gatto1.2k
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 [[alternative HTML version deleted]]
ADD REPLYlink written 6.2 years ago by Reema Singh570
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/
ADD REPLYlink written 6.2 years ago by Laurent Gatto1.2k
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