[BioC] adjusted p values

[Naomi Altman]

I am not completely sure about 2, but you have interpreted 1 
correctly.  I don't think we should call these "adjusted p-values" 
because they are not, but this terminology seems to be used.

--Naomi

At 09:15 PM 6/18/2007, Lev Soinov wrote:
>Dear List,
>
>   I've got a bit confused reading previous discussions from the 
> list on the terminology about q values, adjusted p values and FDR 
> in the LIMMA. Please, could you correct me if I am wrong here:
>   1. BH adjusted p values from topTable or from decideTests are 
> actually FDR. So, if we select genes with adjusted p values <0.05 
> then we estimate that 5% of the selected genes are not really 
> differentially expressed, i.e. false positives.
>   2. when using decideTests with method="nestedF", p.value =0.01 
> and adjust.method="BH", does it give you the list of genes for 
> which BH adjusted F.p values <0.01, so one should expect 1% of 
> false positive results in the list of the selected genes?
>
>   With kind regards,
>   Lev.
>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
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