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Question: using camera/roast/romer to find enriched gene sets from proteomics data
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gravatar for natalia.pietrosemoli
13 months ago by
natalia.pietrosemoli0 wrote:

Dear all,

 

I'm perfoming a proteomics analysis (using limma-voom) to get differentially expressed proteins among several conditions.

Could I also benefit from the gene set tests in the limma package as well (provided that I make the necessary adjustments from proteins to gene ids?)

 

Thanks a  lot,

Bioinformatitian in distress

ADD COMMENTlink modified 13 months ago by Gordon Smyth32k • written 13 months ago by natalia.pietrosemoli0
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gravatar for Gordon Smyth
13 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Yes, of course, you could use gene set tests for proteomics data.

The real question, which you don't mention in your post, is why you are having trouble with that, i.e., why are you "in distress"?

A side question is why you are using voom for proteomics data. The limma authors recommend limma-trend rather than limma-voom for proteomics data. See voom for spectral counts

ADD COMMENTlink modified 13 months ago • written 13 months ago by Gordon Smyth32k

Dear Gordon,

Thanks so much for your quick response. In fact, you are right. I tried voom and then I realised it was not apprapriate, so I'm not using it anymore, but I did this part of the anlysis long ago, and had forgotten about it.

I was in distress becuase I had a moment of 'phylosophical' doubt where I was afraid that the methods were not compatible with proteomics data. This is the rist time I work with such type of data.

 

ADD REPLYlink written 13 months ago by natalia.pietrosemoli0
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