[BioC] total count filter cutoff
Wolfgang Huber
whuber at embl.de
Wed Apr 30 20:47:32 CEST 2014
Dear Mahnaz
http://bioconductor.org/packages/release/bioc/html/genefilter.html -> Diagnostics for independent filtering -> Section 4 provides some options.
Wolfgang
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,
> Mahnaz
>
> -- output of sessionInfo():
>
> R 3.0.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
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