[BioC] limma for spectral counts

Laurent Gatto laurent.gatto at gmail.com
Wed Oct 20 17:23:53 CEST 2010

Dear Yolande,

The spectral counts should indeed be normalised but, as far as I know,
there is no direct way to do this in Bioconductor. It should however
not be too difficult to implement if you have the sequence to
normalise the count to the length of the protein. You might also want
to have a look at the emPAI [1] to assess protein abundance from
spectral counts. The emPAI values will probably need some log
transformation before using limma.

If you want to use normalised spectral counts, another option would be
to investigate the use of RNA-seq methods that are meant to work with
counts. edgeR mentions spectral counts in the publication [2], but I'm
sure other Bioconductor packages can equally apply (see for instance
the RNAseq Bioc view).

Hope this helps.

Best wishes,


[1] http://bioinformatics.oxfordjournals.org/content/26/4/576.abstract
[2] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/
[3] http://www.bioconductor.org/help/bioc-views/2.7/BiocViews.html#___RNAseq

Laurent Gatto
Cambridge Centre For Proteomics

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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