[BioC] EdgeR

Gordon K Smyth smyth at wehi.EDU.AU
Thu Aug 29 07:18:05 CEST 2013

Dear Joanne,

If I understand you correctly, you want to filter features based on cpm, 
but you want edgeR to present to the results to you as if you hadn't 
filtered.  No, edgeR doesn't do that.  So keeping track of which windows 
you filtered for the DE analysis is your responsibility.

Best wishes

On Wed, 28 Aug 2013, Joanne.Lee at csiro.au wrote:

> I'm using EdgeR to find differentially expressed reads within 100bp 
> windows. To help my analysis later on I'd like EdgeR to give me an 
> output that contains every 100bp window I have regardless of if it's 
> differentially expressed or not. I'd still like to filter>1CPM, 
> normalise and have differential expression calculated. So I'l like to 
> have the DE recorded as done for the 77811 rows but also have the 
> remaining 2315534 rows (total 2393345 windows - 77811 DE windows) 
> displaying zero.
> I've attached a log of what I normally do to get differentially 
> expressed read output. I'm sure it's just one tiny parameter I should 
> change. Any help on how to get the expression data back from all 2393345 
> windows would be really appreciated!
> Thanks,
> Joanne

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