[BioC] Unequally spaced replicates in limma

Gordon K Smyth smyth at wehi.EDU.AU
Thu Sep 2 00:11:57 CEST 2004

> Hi
> As I have varying numbers of replicates, and they are not regularly
> spaced on the array, and given that I would like a list of
> differentially expressed genes which is averaged over replicates,

I assume that these are within-array replicates.

> I
> assume the best thing to do is normalise my data, and then average over
> replicates in the MAList object, and then pass the averaged data to
> lmFit() etc?

Yes, you could do that.  It does raise subtle issues though concerning how the variance of the
averages depends on the number of replicates.  You might like to compute weights based on the
number of replicates for each probe and pass that to lmFit also.


> Is that right?
> Cheers
> Mick

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