[BioC] total count filter cutoff
Ryan C. Thompson
rct at thompsonclan.org
Wed Apr 30 21:23:45 CEST 2014
Total count filtering and mean count filtering are equivalent, since
the only difference is a constant factor (dividing by number of
samples), so the mean count filter demonstrated in the genefilter
vignette corresponds to your question.
If you are expecting the vignette to simply give you a specific number
to use a as a cutoff, that's not possible, because the threshold
depends on the data. I suggest that you adapt the R code in this
vignette to your data in order to choose an appropriate cutoff.
On Wed 30 Apr 2014 12:04:33 PM PDT, Mahnaz Kiani wrote:
> Thanks for quick response, I did check that but didn't find any information
> about total count filter cutoff, would you please help me with that.
> On Wed, Apr 30, 2014 at 1:47 PM, Wolfgang Huber <whuber at embl.de> wrote:
>> Dear Mahnaz
>> http://bioconductor.org/packages/release/bioc/html/genefilter.html ->
>> Diagnostics for independent filtering -> Section 4 provides some options.
>> Il giorno 30 Apr 2014, alle ore 20:29, mahnaz Kiani [guest] <
>> guest at bioconductor.org> ha scritto:
>>> I'm using edgeR for analysis of may data and I'm not sure what total
>> count filter value cutoff value I should use, My reads are paired 50bP
>> reads and total reads per sample is about 80,000,000. I tried cutoff values
>> of 5,10,15,30,50 and 100 and I only saw differences between 50 and 100 but
>> still looking for logical reason to chose the cutoff value.
>>> Appreciate your help,
>>> -- output of sessionInfo():
>>> R 3.0.2
>>> Sent via the guest posting facility at bioconductor.org.
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