Thanks Simon for your helpful prompt answer
Mali

On Thu, May 31, 2012 at 9:35 AM, Simon Anders <anders@embl.de> wrote:

> Hi Mali
>
>
> 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
>> analysis)?
>>
>
> 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.
>
>  Simon
>
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