[BioC] RNA-Seq, generate batch-free count matrix

[Brian Haas]

Thanks, Gordon!  If I want to also remove effects related to total read counts or coverage biases or other library quality metrics, which sometimes end up being highly correlated with principal component 1, do I include these continuous values as covariates in the removeBatchEffect() method?  I was looking for some examples on how to use it, but couldn't find any.

Thx
-Brian



> On Jul 20, 2014, at 8:18 PM, Gordon K Smyth <smyth at wehi.EDU.AU> wrote:
> 
> 
>> On Mon, 21 Jul 2014, Gordon K Smyth wrote:
>> 
>> logCPMc <- removeBatchEffect(y, batch)
> 
> Should have written
> 
> logCPMc <- removeBatchEffect(y2, batch)
> 
> Gordon
> 
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