[BioC] Using limma for quantitative proteomics data

[Yong Li]

Dear Aaron,

thank you for your quick answer! I have checked the help page of
voom() but it seems to be used for count data. My data are just
tumor/normal ratios. I am wondering if you could provide more details?

Best regards,
Yong

On Tue, Jun 19, 2012 at 8:18 PM, Aaron Mackey <amackey at virginia.edu> wrote:
> 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 at 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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>