[BioC] DESEQ ANODEV : A time course study

Simon Anders anders at embl.de
Mon Jun 10 08:41:49 CEST 2013

Hi Michael

On 08/06/13 03:00, Michael Breen wrote:
> What we aim to do is to test for DE of transcripts across all 3 time
> points for disease and controls seperatly (using DESeq ANODEV) but we want
> to be able to identify at which
> time points these transcripts are being DE. In other words, we want to
> compare DE transcripts with
> respect to specific time points between cases and controls. Our remaining
> code looks like this:
> fit0 <- fitNbinomGLMs (cds, count ~ timecourse)
> fit1 <- fitNbinomGLMs ( cds, count ~ timecourse + condition )
> str(fit1)

One possibility would be to subset your data to only samples from one 
time point and then test cases against control to see the genes that are 
DE at this time point, then go on to the next one. If you consider this 
a post-hoc test and only look at the genes which show overall 
sensitivity, you can probably be more lenient on the significance 
threshold. Maybe other people on the list have input on this point.


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