[BioC] XCMS for LC-MS

Bashar Amer Bashar.Amer at agrsci.dk
Fri Dec 20 12:03:46 CET 2013


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.


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)

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