Hello list
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)?
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?
Thanks
Mali
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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
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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