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Question: limma; Only fit list of certain genes/ filter eSet
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gravatar for bi_Scholar
2.2 years ago by
bi_Scholar0
bi_Scholar0 wrote:

Hello,

I got a list of genes (<1000) for which I want to perform DEG-Analysis. Since I'm only interested in certain genes, I want to filter out the rest to reduce false-negative results and get more information about the genes I'm actually interested in.

Is there a simple way to do this with limma, or can I somehow filter genes from a expression set? If I try to fit a exprs-Matrix instead of a exprs-Set, I'm excluding genenames, GO annotations, etc. which is very unpleasant.

Thanks in advance!
 

ADD COMMENTlink modified 2.2 years ago by Gordon Smyth35k • written 2.2 years ago by bi_Scholar0
4
gravatar for Gordon Smyth
2.2 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

Yes, there's a simple way to do it. Just do the usual linear model analysis using all the expressed genes, not just your focus set of interest. Then make the topTable just for your set of interest:

topTable( fit[mygenes, ], coef=whatever)

where mygenes selects your genes of interest and "whatever" is the contrast you want to test for. mygenes can be a vector of row names, or a TRUE/FALSE vector, or a vector of row numbers.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Gordon Smyth35k

Perfect. Thanks alot!

ADD REPLYlink written 2.2 years ago by bi_Scholar0
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