[BioC] Using limma for quantitative proteomics data

[Bernd Fischer]

Dear Yong!

I used limma for ion count data. First I computed log-ratios per peptide and
then summarized log-ratios per protein. Protein log-ratios were then 
analyzed
by limma.
Have a lock at our paper:
Castello, Fischer, et al., Insights into RNA Biology from an Atlas of 
Mammalian
mRNA-Binding Proteins, CELL, 2012

Best,
Bernd


On 06/19/2012 06:47 PM, Yong Li wrote:
> Hello,
>
> limma has been so valuable in microarray data analysis, but has anyone
> used limma for finding differentially expressed proteins from
> quantitative proteomics data? The data I got has tumor/normal ratios
> of thousands proteins, and both tumor and normal have a number of
> replicates. Could such data be analyzed with limma?
>
> If limma can not be used here, what statistics method is suitable so
> that we can get statistically significant proteins with p-values? Any
> suggestion is appreciated.
>
> Kind regards,
> Yong
>
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