[BioC] edgeR: deDGE Fisher exact p-values

[Daniel Brewer]

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
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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