[BioC] DEXSeq filtering
anders at embl.de
Thu May 31 08:35:39 CEST 2012
On 2012-05-31 07:47, mali salmon wrote:
> Two questions regarding DEXseq
> 1. Would you recommend to do an independent filtering prior to differential
> exon expression analysis (similar to what is done with gene expression
Use the parameter 'minCount' in estimateDispersions for this. The
default, 10, is probably reasonable, but maybe a bit on the low end.
Every exon with less than 10 counts (summed across all sample) is
omitted from the tests.
> 2. What about exons with 0 counts across all samples, does DEXSeq uses them
> when estimating overall gene expression? would you recommend to remove
> those before analysis?
No need to remove them manually, estimateDispersion does this anyway.
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