[BioC] Reproducibility in DESeq

[Simon Anders]

Hi,

On 07/11/2012 11:00 AM, Fatemehsadat Seyednasrollah wrote:
> I have several subsets of a datasets from one RNA seq experiment and
> I need to compare the reproducibility of these different subsets with
> DESeq. I have both FDR and P values for each gene in my subsets and I
> need to transform P value or FDR to RANK coordination. Then I can
> plot the reproducibility(y axis) according to this rank(x axis) which
> has obtained from p value or FDR for each differentially expressed
> gene. Any idea for transforming one of these parameters to obtain a
> rank?(I should transform p value or fdr to this rank and use it as x
> axis of my plot).

To convert a list of values to ranks in R, simply use the 'rank' function.

However, I am rather sceptical that comapring ranks of p values is a 
suitable method to assess reproducibility of an experiment.

   Simon