[BioC] edgeR: deDGE Fisher exact p-values

[Mark Robinson]

Hi Daniel.

Thanks for the note.  Indeed, there was a change in the package there  
as to where the exact p-values get calculated.  I have mixed feeling  
on this, but the decision to move this to topTags() was based on the  
fact that we now support multiple groups yet the exact test is only  
realistic for 2-group comparisons.  In topTags(), you must specify the  
pairwise difference of interest.  I would welcome your feedback on  
this design decision as like I said, I have mixed feelings of how this  
should be done.  The alternative is to precompute all the pairwise  
exact tests in deDGE() and maintain the $exact element.

As to the vignette example, I suspect you are using an older  
vignette.  The vignette for 1.2.x illustrates the same example with  
updated code.

Hope that helps.
Mark


On 12-Aug-09, at 8:57 PM, Daniel Brewer wrote:

> It use to be that when you run deDGE from the edgeR library that it
> calculated the Fisher exact p-values and put it in a slot "exact".   
> This
> no longer seems to be the case, with the p-values only being  
> calculated
> when topTags() is called.  This means that the plot example in the
> vignette no longer works i.e.
>
>> adj.p <- p.adjust(ms$exact, "fdr")
>> k <- (adj.p < 0.05)
>> plotMA(ms, col = c("black", "blue")[k + 1])
>
> Have I missed something?  How do you get round this?
>
> Thanks
>
> Dan
>
> -- 
> **************************************************************
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
> Email: daniel.brewer at icr.ac.uk
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