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

[Gordon K Smyth]

Yes, just input continuous variable as covariates.

Gordon

----- Original Message -----
From: "Brian Haas" <bhaas at broadinstitute.org>
To: "Gordon K Smyth" <smyth at wehi.edu.au>
Cc: "Bioconductor mailing list" <bioconductor at r-project.org>
Sent: Monday, 21 July, 2014 11:48:49 AM
Subject: Re: RNA-Seq, generate batch-free count matrix

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

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