Question: XCMS for LC-MS
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5.8 years ago by
Guest User12k
Guest User12k 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.
xcms • 1.1k views
ADD COMMENTlink modified 5.8 years ago by Bashar Amer20 • written 5.8 years ago by Guest User12k
Answer: XCMS for LC-MS
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gravatar for Bashar Amer
5.8 years ago by
Bashar Amer20
Bashar Amer20 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
ADD COMMENTlink written 5.8 years ago by Bashar Amer20
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
ADD REPLYlink written 5.8 years ago by Ivan Gregoretti310
Answer: XCMS for LC-MS
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gravatar for Kasper Daniel Hansen
5.8 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
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]]
ADD COMMENTlink written 5.8 years ago by Kasper Daniel Hansen6.4k
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
ADD REPLYlink written 5.8 years ago by Bashar Amer20
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
ADD REPLYlink written 5.8 years ago by James W. MacDonald51k
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