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Question: Random effects with limma's camera()
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gravatar for Stephen Hoang
2.6 years ago by
Stephen Hoang30 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 

ADD COMMENTlink modified 2.6 years ago by Gordon Smyth35k • written 2.6 years ago by Stephen Hoang30
1
gravatar for Gordon Smyth
2.6 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k 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 COMMENTlink modified 2.6 years ago • written 2.6 years ago by Gordon Smyth35k
2

Can this now be addressed by using the recent pre-ranked cameraPR() function? i.e. run lmFit() with block and correlation, then eBayes() (or treat() if appropriate?) and use the t-statistics.

ADD REPLYlink written 11 months ago by jamie.gearing40

Yes, that's right (as long as you're happy with a preset value for the inter-gene correlation).

ADD REPLYlink written 11 months ago by Gordon Smyth35k

Thanks Gordon.

ADD REPLYlink written 10 months ago by jamie.gearing40
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