[BioC] DEXSeq all p-values are 1

[Steve Lianoglou]

Hi,

It's hard to provide any meaningful help, since we really don't have
any information about your data, or what you code (code examples) to
identify a problem.

But:

On Thu, Dec 13, 2012 at 10:08 AM, Philip [guest] <guest at bioconductor.org> wrote:
>
> Hello,
>
> I'm trying to use DEXSeq to identify alternative exon usage. Using DESeq I've identified ~200 differentially expressed genes in my gene set. I've basically applied the guidelines from the manual to my data set - single reads in duplicates +/- treatment.

Does that mean you have 4, singe end read runs? 2 biological
replicates for (+) treatment, and 2 for (-) treatment?

> I've played around with the parameters in different ways,

Which parameters?
What ways?
How did you count reads / bin?
How did you define the bins?

> but no matter how I do it the adjusted p-values all come out as 1 or N/A. The non-adjusted p-values are pretty high, so I reckon the adjusted p-values are "true", however, when I go true single genes I find exons that have really high fold-change values indicating differential expression.

High dispersion values can make high fold changes statistically insignificant.

Did you explore the quality of your replicates? How? How do they look?

> Is this a result one can expect (due to e.g. high variance in replicates)

That can explain it.

There is, of course, always the possibility that there is very little
differential splicing in your experiment.

> or is it possible that something is wrong in my analysis?

It is always possible that there is something wrong with an analysis.
As I mentioned at the start, without knowing more about your analysis
and seeing the code, there is no way that anybody can answer this
question.

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact