[BioC] decideTests limitation to certain lfc and p values not working

[Alex Gutteridge]

On Tue, 9 Nov 2010 15:24:48 +0100, Moritz Kebschull <endothel at gmail.com>
wrote:
> Dear list,
> 
> I am comparing cells with a gene knockdown with wildtype cells to find
> genes
> differentially regulated in response to the knockdown using Illumina
bead
> arrays. I plan to compare genes regulated by CPT stimulation in
knockdown
> and wildtype cells. For that, I used a Venn Diagram, and export a list
of
> the genes of the knockdown only category.
> However, whatever I enter for lfc in the decideTests function, the
numbers
> of genes in the resulting diagram stay the same, whilst from manual
> comparison of the data, they should not. Does anyone know what I am
doing
> wrong?
> 

[snip]

>
decideTests(ebFit,method="separate",adjust.method="BH",p.value=0.05,lfc=1)
> results=decideTests(ebFit)
> a <- vennCounts(results)

Look closely at these lines!

-- 
Alex Gutteridge