Hey Matt, 

I have never used the ERCC controls, so maybe my comments aren't useful to you. However, we have done a lot of work with normalizing arrays based on control probes, and I have to say that I have never truly been satisfied. However, we have been very successful in using inactive genes/probes for actual genes on the array for normalizing arrays. Our recent SCAN normalization (http://www.ncbi.nlm.nih.gov/pubmed/22959562)  is designed identify inactive genes on each individual array, and then use these probes to do the normalization. It works extremely well and will outperform both RMA and dChip. Also, there's an easy to use Bioconductor package (SCAN.UPC) since that's what you prefer to use.

I know it doesn't answer your question directly, but hopefully its helpful.

Thanks!

Evan  


On Nov 20, 2012, at 6:00 AM, bioconductor-request@r-project.org wrote:

> Date: Tue, 20 Nov 2012 00:26:39 +0000
> From: "Thornton, Matthew" <Matthew.Thornton@med.usc.edu>
> To: "bioconductor@r-project.org" <bioconductor@r-project.org>
> Subject: [BioC] Normalizing affymetrix chips with ERCC
> Message-ID:
> 	<AD53D86BA0E3974B908175E10777B27E1D7606C1@MED-MBX2.med.usc.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hello,
> 
> I was wondering if anyone had been using the ERCC controls from Ambion with Affymetrix human gene ST arrays? I guess there are probes sets on the chips for them, but there isn't much in the literature about anyone actually using them. I am thinking that it would be better to process the data using dchip, but I would rather use R and bioconductor.  Any comments are welcome!
> 
> TIA
> 
> Matt


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