yes, it should be possible with a voom()-based analysis to get the
variances "right".

-Aaron

On Tue, Jun 19, 2012 at 12:47 PM, Yong Li <mail.yong.li@googlemail.com>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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