[BioC] XCMS for LC-MS

[James W. MacDonald]

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>.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099