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Question: Random effects with limma's camera()
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gravatar for Stephen Hoang
16 months ago by
Stephen Hoang • 30
Stephen Hoang • 30 wrote:

Hi All,

Is there a way to incorporate the consensus correlation calculated by duplicateCorrelation() into the gene set enrichment test performed by camera()? In short, I would like to treat one of my factors as a random effect via duplicateCorrelation() (this is what I did for differential expression testing). As far as I can tell, camera() is only aware of fixed effects. I don't have the option of treating my random effect as a fixed effect because I end up with a design matrix that is not of full rank. It seems like my only option is to run camera() using only fixed effects, and treat the results as overly-conservative.

Thanks in advance,

Steve 
limma camera duplicatecorrelation
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modified 16 months ago by Gordon Smyth ♦ 30k • written 16 months ago by Stephen Hoang • 30
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gravatar for Gordon Smyth
16 months ago by
Gordon Smyth ♦ 30k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth ♦ 30k wrote:

Sorry, you can't use duplicateCorrelation() with camera(). It has been on my to-do list for a while, but I haven't managed to find time to develop and implement it.

You can use duplicateCorrelation() with roast(), mroast() or romer().
ADD COMMENT • link modified 16 months ago • written 16 months ago by Gordon Smyth ♦ 30k
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