[BioC] XCMS for LC-MS

[Ivan Gregoretti]

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
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