[BioC] Using limma for quantitative proteomics data

[Yong Li]

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