Question

using camera/roast/romer to find enriched gene sets from proteomics data

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natalia.pietrosemoli • 0

@nataliapietrosemoli-10587

Last seen 7.2 years ago

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

limma proteomics camera mroast romer • 1.5k views

ADD COMMENT • link updated 7.5 years ago by Gordon Smyth 50k • written 7.5 years ago by natalia.pietrosemoli • 0

score 0 · Answer 1 · 2016-10-04

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Gordon Smyth 50k

@gordon-smyth

Last seen 9 minutes ago

WEHI, Melbourne, Australia

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 COMMENT • link 7.5 years ago Gordon Smyth 50k

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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 REPLY • link 7.5 years ago natalia.pietrosemoli • 0