[BioC] averaging replicates within arrays

[Gordon K Smyth]

On Thu, November 10, 2005 4:33 am, Naomi Altman wrote:
> I am facing a similar problem, and here is what I plan.  (I am
> putting out this suggestion for general discussion).
>
> Step 1: Use duplicateCorrelation in limma.  The genes with 6 spots
> will be treated as 2 groups of 3.  We need equal groups for the eBayes step.
>
> Step 2: Adjust the eBayes estimate of variance for 6 spots instead of
> 3.  Compute all the contrasts using all 6 spots, and write a bit of
> code to redo the tests on the 6 spots data.
>
> I think this is better than using the extra spots to check the
> consistency of results, as has been suggested previously on this
> list.  We have more spots for some genes because, given the space on
> the array, we did extra duplication of genes that were of primary
> interest.  We ought to use the increased power this gives us.
>
> --Naomi
>
> p.s. In our case, we have either 1 or 2 spots per gene.  In designing
> an array, I probably would use 4 spots for every gene rather than 3
> for some and 6 for others.

That seems a well motivated approach to me.

Cheers
Gordon