XCMS for LC-MS
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Last seen 10.2 years ago
I am a user of XCMS for analysing LC-MS data. I have 500 samples(chromatograms) and I am getting an error message when ever I start the analysis saying cant make a vector of some MB size. I got the message after applying this command, it Works for some samples but at some point it stops: > xset <- xcmsSet(myDir, ppm = 25, peakwidth = c(20,50), method ="centWave", snthresh = 10, prefilter = c(3,100), mzCenterFun ="wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE) would you please help me and inform me how i woud be possible increasing the capacity, -- output of sessionInfo(): (Error: cannot allocate vector of size 225.3 Mb) -- Sent via the guest posting facility at bioconductor.org.
xcms xcms • 2.1k views
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Bashar Amer ▴ 20
@bashar-amer-6298
Last seen 10.2 years ago
Dear Sir/Madam, I am a user of XCMS for analysing LC-MS data. I have 500 samples (chromatograms) and I am getting an error message when ever I start the analysis saying cant make a vector of some MB size. I got the message after applying this command, it Works for some samples but at some point it stops: xset <- xcmsSet(myDir, ppm = 25, peakwidth = c(20,50), method = "centWave", snthresh = 10, prefilter = c(3,100), mzCenterFun ="wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE) would you please help me and inform me how i woud be possible increasing the capacity, Kind Regards, Bashar Amer Bashar Amer PhD Student, Department of Food Science, Aarhus University
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Hello Bashar, I am unfamiliar to LC-MS with R but a common problem is trying to load in memory a vector that is too big for the hardware or software that you have. To help people help you, I suggest that you execute sessionInfo() at the R prompt and copy/paste that information so that we can at least see whether you are using a 32bit or a 64bit version. Also, copying and pasting the error message exactly as it is, may help. Cheers, Ivan Ivan Gregoretti, PhD Bioinformatics On Fri, Dec 20, 2013 at 3:00 AM, Bashar Amer <bashar.amer at="" agrsci.dk=""> wrote: > Dear Sir/Madam, > > I am a user of XCMS for analysing LC-MS data. I have 500 samples > (chromatograms) and I am getting an error message when ever I start > the analysis saying cant make a vector of some MB size. > > I got the message after applying this command, it Works for some > samples but at some point it stops: > > xset <- xcmsSet(myDir, ppm = 25, peakwidth = c(20,50), method = "centWave", snthresh = 10, prefilter = c(3,100), mzCenterFun ="wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE) > > would you please help me and inform me how i woud be possible > increasing the capacity, > > Kind Regards, > Bashar Amer > > > > Bashar Amer > > PhD Student, > Department of Food Science, Aarhus University > _______________________________________________ > 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
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@kasper-daniel-hansen-2979
Last seen 17 months ago
United States
You don't have enough RAM. Kasper On Fri, Dec 20, 2013 at 9:09 AM, Bashar Amer [guest] <guest@bioconductor.org> wrote: > > I am a user of XCMS for analysing LC-MS data. I have 500 > samples(chromatograms) and I am getting an error message when ever I start > the analysis saying cant make a vector of some MB size. > I got the message after applying this command, it Works for some samples > but at some point it stops: > > > xset <- xcmsSet(myDir, ppm = 25, peakwidth = c(20,50), method > ="centWave", snthresh = 10, prefilter = c(3,100), mzCenterFun ="wMean", > integrate = 1, mzdiff = -0.001, fitgauss = FALSE) > > > would you please help me and inform me how i woud be possible increasing > the capacity, > > > -- output of sessionInfo(): > > (Error: cannot allocate vector of size 225.3 Mb) > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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Hi, so does it Means I need to use a computer with higher RAM? Bashar Amer PhD Student, Department of Food Science, Aarhus University ________________________________________ From: Kasper Daniel Hansen [kasperdanielhansen@gmail.com] Sent: Friday, December 20, 2013 11:43 AM To: Bashar Amer [guest] Cc: bioconductor at r-project.org; Bashar Amer; xcms Maintainer Subject: Re: [BioC] XCMS for LC-MS You don't have enough RAM. Kasper On Fri, Dec 20, 2013 at 9:09 AM, Bashar Amer [guest] <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> wrote: I am a user of XCMS for analysing LC-MS data. I have 500 samples(chromatograms) and I am getting an error message when ever I start the analysis saying cant make a vector of some MB size. I got the message after applying this command, it Works for some samples but at some point it stops: > xset <- xcmsSet(myDir, ppm = 25, peakwidth = c(20,50), method ="centWave", snthresh = 10, prefilter = c(3,100), mzCenterFun ="wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE) would you please help me and inform me how i woud be possible increasing the capacity, -- output of sessionInfo(): (Error: cannot allocate vector of size 225.3 Mb) -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Bashar, It means you need more RAM. Whether you find a different machine with more RAM or install more RAM in the computer you are using is up to you. Best, Jim On 12/20/2013 6:03 AM, Bashar Amer wrote: > Hi, > > so does it Means I need to use a computer with higher RAM? > > Bashar Amer > > PhD Student, > Department of Food Science, Aarhus University > ________________________________________ > From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com] > Sent: Friday, December 20, 2013 11:43 AM > To: Bashar Amer [guest] > Cc: bioconductor at r-project.org; Bashar Amer; xcms Maintainer > Subject: Re: [BioC] XCMS for LC-MS > > You don't have enough RAM. > > Kasper > > > On Fri, Dec 20, 2013 at 9:09 AM, Bashar Amer [guest] <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> wrote: > > I am a user of XCMS for analysing LC-MS data. I have 500 samples(chromatograms) and I am getting an error message when ever I start the analysis saying cant make a vector of some MB size. > I got the message after applying this command, it Works for some samples but at some point it stops: > >> xset <- xcmsSet(myDir, ppm = 25, peakwidth = c(20,50), method ="centWave", snthresh = 10, prefilter = c(3,100), mzCenterFun ="wMean", integrate = 1, mzdiff = -0.001, fitgauss = FALSE) > > would you please help me and inform me how i woud be possible increasing the capacity, > > > -- output of sessionInfo(): > > (Error: cannot allocate vector of size 225.3 Mb) > > -- > Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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