[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)

Sorry, if my previous post was too cryptic. I know if you stare at these
things long enough you miss the wood for the trees. You need to assign the
result of your first call to decideTests() to uh... "results". And then
remove the second call to decideTests(). E.g.

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

Should get you where you want to be.

-- 
Alex Gutteridge