[BioC] limma for spectral counts

[Pavelka, Norman]

Hi Yolande,

You can try normalizing your specral counts following the NSAF (Normalized Spectral Abundance Factor) approach and then you can use package 'plgem' to detect your differentially abundant proteins. You can have a look at this publication to get an idea and then let me know if you need any help:

http://www.ncbi.nlm.nih.gov/pubmed/18029349

Thanks and good luck!
Norman


On 20 October 2010 14:20, Yolande Tra <yolande.tra at gmail.com> wrote:
> Hello list members,
>
> I was wondering if limma method can be used for spectral counts of
> proteins from mass spectrometry. If yes, is there a function in
> Bioconductor that normalizes these counts.before running limma.
>
> Thank you for your help,
>
> Yolande
>
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Norman Pavelka, Ph.D.
Postdoctoral Research Associate
Rong Li lab
Stowers Institute for Medical Research
1000 E. 50th St.
Kansas City, MO 64110
U.S.A.
 
phone: +1 (816) 926-4103
fax: +1 (816) 926-4658
e-mail: nxp at stowers.org