[BioC] FW: Limma p-values, fdr and classifyTests

[Gordon Smyth]

At 11:53 PM 23/08/2004, Matthew  Hannah wrote:
>Sorry I'd been away and missed some posts - it seems limma - fdr is a
>hot topic at the moment.
>
>To link this to an answer already provided by gordon - this is the
>thread I found earlier -
>https://www.stat.math.ethz.ch/pipermail/bioconductor/2004-August/005616.
>html
>
>This addresses possibilities to fdr correct on the gene and contrast
>level, however I was wondering if anyone can confirm that the fdr in
>toptable is on the gene level.

The adjustment is across genes. It can only be across genes because 
topTable considers only one contrast at a time.

>  If so can the vector of p-values be
>passed back to classifytests to put the 1 / -1's in for those up / down
>reg?

No

>  Also is there any difference in doing contrasts then genes vs. the
>reverse?

Yes.

>I'd also be interested in the discussion of how quantitive limma
>p-values are (see point 4 in previous mail below).

Too big a question for here. The p-values could be believed if the 
heirarchical model is correct, but no models are correct for microarray data.

>On these lines - from the abstract of Smyth. LM and eBayes methods...
>"The eBayes approach is equilivent to shrinkage of the estimated sample
>variances towards a pooled estimate.." I assume (as it works with low
>#'s of arrays) that the pooled estimate is between genes rather than
>arrays? If so then what about pooling between arrays - eg: when you have
>10 lines exposed to a common treatment and say 3 reps. So 10x2 x3reps.
>Using the pooled estimate across arrays (30reps control vs. 30 reps
>treated) to then apply to differences between lines due to the treatment
>(only 3 vs. 3 arrays)? Obviously the lines would have to be generally
>similar. But wouldn't this be more biologically relevent than assuming
>similar expressed genes have similar variance?

The variances are already pooled across arrays. There is no assumption that 
"similar expressed genes have similar variances".

Gordon

>Thanks in advance,
>Matt