[BioC] decideTests with nestedF

Pedro López Romero plopez at cnic.es
Fri Jun 16 17:57:07 CEST 2006

Hi Jim, 

> Not sure I understand your point. Are you saying that a particular 
> contrast that appears to be significant using your method ends up having 
> a very large p-value if you use nestedF?

Not exactly. The problem is that using decideTests(..., method="nestedF")
with the whole set of genes  (not filtered by any method), some of the
selected genes have an adjusted p-value quite large, corresponds to genes
with a very small M value.- Theses genes are in the list of differentially
exprssed genes  selected with decideTests(..., method="nestedF").

For example, here I show you two of the genes for a particular contrast that
would be selected using decideTests(...,method="nestedF" )

	M	A		t		P.Val		adj.P.Val
1.064610409	13.0019494	4.18633292	0.000240894	0.239943977
0.489386597	8.228402648	2.86816475	0.007621841	0.817992583

I am a bit confused with this result?, Any clue? 


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