[BioC] RNA-Seq, generate batch-free count matrix
Brian Haas
bhaas at broadinstitute.org
Mon Jul 21 03:48:49 CEST 2014
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
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:6}}
More information about the Bioconductor
mailing list