Chris, 

Looking at your plots: Don't re-quantile normalize your data. It turns out that QQ norm can actually introduce artifacts into the data on occasion. Your plots look okay to me, so I strongly recommend that you use the data 'as is' after ComBat.

Evan



On Nov 5, 2012, at 11:12 AM, chris briggs wrote:

> I have 3 different tumor categories (Cap, Ece and R1)  each with an equal number of -T (tumor derived mRNA) and -N (adjacent normal-tissue derived mRNA) for each tumor category. Each array is a batch, as shown in the attached Combat Sample Table. Does it look correct? I've also attached the density plot for my Combat corrected data. Recall that I used log2 transformed, quant. normalized data for the Combat correction.
> 
> Thanks,
> Chris
> 
> 
> 
> On Sat, Nov 3, 2012 at 4:05 PM, W. Evan Johnson <wej@bu.edu> wrote:
> 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
> 
> 
> 
> 
> -- 
> cell phone: 617 905-9301
> office phone: 617 779-6535
> FAX: 617 779-6572
> office emails: christine.briggs@steward.org
> 
>  
> 
> <Cmbat_SampleTable_103012.txt><DensityPlot_Lg2QnCombat_Values.pdf>


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