[BioC] pvalue and padj in DESeq

[Simon Anders]

Hi

On 2012-06-26 15:58, narges [guest] wrote:
> i have a proper count table of RNA-Seq and i have applied edgeR package for obtaining differentially expressed genes and I have obtained nice acceptable result.
> But now I am applying also DESeq over the same data but the pval and padj columns of the nbinomTest over them is strange, it is almost 1.00 or NA.

> Why is this so?

You know, we are not clairvoyants. Without any more information about 
your experiment and data, and without seeing the R code that you used to 
perform the analyses, any answer would just be guessing.

Most likely you made a mistake in using the software. Or, maybe the two 
tools do come to different conclusions about the signal-to-noise ratio 
of your data.

EdgeR and DESeq use similar but not identical methods. I understand that 
you prefer the result that says that your experiment worked, but this 
does not seem a good argument to decide which method is correct.

   Simon