[BioC] DEXSeq - identical p-values for all exons in a gene

Simon Anders anders at embl.de
Mon Jan 20 09:15:28 CET 2014

Hi Katherine

On 19/01/14 23:34, Pillman, Katherine (Health) wrote:
> Thanks for your response to my message.  I'm sorry but I don't
> understand what you mean (perhaps this is the root of my problem!).
> You wrote that I did not specify the full model formula to
> estimateDispersions.  I am confused because I thought that was what I
> was doing when I wrote "formula=formulaFullModel" in the line:
>>> ecs <- estimateDispersions(ecs, formula=formulaFullModel,
>>> nCores=cores, quiet=FALSE, file='dexseq_progress_report.txt')

Actually, this line is correct and does contain the formula as it
should. Not sure, how I have overlooked this last time. Very sorry!

So, your problem must lie somewhere else. Maybe something is wrong with
the counts. Could you post the output of "countTableForGene" for one of
the genes that have all identical p values?

   countTableForGene( ecs, "A1BG", normalized=FALSE )
   countTableForGene( ecs, "A1BG", normalized=TRUE )

Maybe also post the full code and sample tables once more, because there
is some strange mismatch: The formulas you posted earlier mention a
factor "libType", which does not appear in your sample table. There, you
have, besides "condition", the factors "type" and "end".


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