Hey Chris, 

My preliminary thought is that its NOT a good idea. 

Are your batches balanced WRT treatment/control? How far are they off? Can you send me a plot?

Evan
 

On Nov 3, 2012, at 7:00 AM, bioconductor-request@r-project.org wrote:

> Message: 8
> Date: Thu, 1 Nov 2012 14:35:48 -0400
> From: chris briggs <cebriggs7135@gmail.com>
> To: bioconductor@r-project.org
> Subject: [BioC] ComBat - pre and post Combat quantile normalization?
> Message-ID:
> 	<CAMuHhE_0r+N4fdPXv+a45c_8nk1rLxQHu89t6iRC8fqZ3jEGFA@mail.gmail.com>
> Content-Type: text/plain
> 
> Dear Evan,
> I ran Combat on my log2 transformed quantile-normalized data (44 samples,
> Illumina HT12) and a density plot of the Combat corrected data showed that
> a second quantile normalization might be in order. The peaks were slightly
> unaligned. Does that sound like a good idea?
> Chris


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