[BioC] total count filter cutoff (edgeR)

[Gordon K Smyth]

Hi Mahnaz,

Why don't you follow the advice of the edgeR User's Guide (as Mark has 
suggested)?  All the case studies in the User's Guide describe how the 
filtering was done in a principled way.

Total count filtering is not so bad, but it is susceptible to being driven 
by one library, especially by one library with a large sequence depth. 
The procedure described by Mark and used in the guide is a compromise of 
several considerations.

BTW, there are newer versions of R and edgeR available than what you are 
using.

Best wishes
Gordon


> Date: Wed, 30 Apr 2014 21:34:50 +0200
> From: Mark Robinson <mark.robinson at imls.uzh.ch>
> To: "Ryan C. Thompson" <rct at thompsonclan.org>
> Cc: bioconductor at r-project.org, Mahnaz Kiani <mahnazkiani at gmail.com>
> Subject: Re: [BioC] total count filter cutoff
>
>
> In my lab, we typically follow a "CPM of at least X in at least Y 
> samples" rule, where X=1 (arbitrary but reasonable, can be changed) and 
> Y=size of smallest replicate group, according to one of the case studies 
> in the user's guide, for example:
>
> ------
> 4.3.6 Filtering

> We filter out very lowly expressed tags, keeping genes that are 
> expressed at a reasonable level in at least one treatment condition. 
> Since the smallest group size is three, we keep genes that achieve at 
> least one count per million (cpm) in at least three samples:
>
>> keep <- rowSums(cpm(y)>1) >= 3
>> y <- y[keep,]
> ------
>
> (http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf)
>
> Cheers, Mark
>
>
> ----------
> Prof. Dr. Mark Robinson
> Statistical Bioinformatics, Institute of Molecular Life Sciences
> University of Zurich
> http://ow.ly/riRea


> Date: Wed, 30 Apr 2014 11:29:28 -0700 (PDT)
> From: "mahnaz Kiani [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, mahnazkiani at gmail.com
> Subject: [BioC] total count filter cutoff
>
>
> 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

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