[BioC] DEXSeq, gene not testable due to 2 out of 84 exons with a low nr of counts

Simon Anders anders at embl.de
Tue Nov 5 14:00:57 CET 2013

Dear Hanneke

On 04/11/13 11:55, Hanneke van Deutekom wrote:
> With 82 testing bins, this gene should have turned out to be testable. I
> removed the two exons with 1 and 3 reads in total, and rerun the program.
> This time the gene turns up to be testable.
> Now, I was highly interested in this particular gene, but I now wonder
> whether I have to remove all exons < 10 reads, in order for the program to
> take along all genes that still might be interesting to look at. Or should
> I just put minCount to 1?

No, you are right, of course, that DEXSeq should have marked only the 
two low-count exons as not testable and keep all the others in the test. 
Maybe you stumbled over a strange bug. Could you perhaps send us by 
email your ExconCountSet, so we can investigate? Please let us also know 
which gene you mean and which DEXSeq version you are using.


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