[BioC] limma for spectral counts

Pavelka, Norman NXP at stowers.org
Sat Oct 23 01:49:56 CEST 2010

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:


Thanks and good luck!

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
phone: +1 (816) 926-4103
fax: +1 (816) 926-4658
e-mail: nxp at stowers.org

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