Hi Manoj,

If you don't do anything special, the normal testForDEU should do what (I
think) you want, which is to test if there is *any* dependence of exon
usage across all conditions at once.

HTH,

-steve

On Thursday, July 11, 2013, Manoj Hariharan wrote:

> Hello,
> I have 37 RNA-seq datasets for 18 human tissues - some have 3 replicates,
> some 2 and some do not have any (sorry to say that).
>
> I'm thinking of a way to do differential exon usage analysis - using
> DEXseq.
>
> I could not see any example in the documentation where multiple
> conditions are compared (eg., tissues) other than pairwise comparisons
> (this is not a case-control kind of study).
> In edgeR, I was able to use the ANOVA-like test for getting
> differentially expressed genes (across all 18 tissues). I
> was wondering if there is such a test I could do with DEXseq.
>
> Thanks,
> Manoj.
>
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-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech

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