[BioC] Using limma for quantitative proteomics data

[Yong Li]

Dear Bernd,

thank you for your answer and the paper. It was mentioned in the paper
that the R script used for the analysis was in a Bioconductor data
package named mRNAinteractomeHeLa, however I couldn't find it on the
Bioc web site. The paper is new so probably I should wait for the next
Bioc release?

Best regards,
Yong

On Wed, Jun 20, 2012 at 8:09 AM, Bernd Fischer <bernd.fischer at embl.de> wrote:
> 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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>
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