Juliet, 

Two thoughts and ideas for you: 

First off, another new alternative to fRMA is SCAN, which is now in press at the journal Genomics. SCAN also works on single samples and it works as well as fRMA without the need to design/use frozen vectors for your particular array platform. Software is available at: http://jlab.bu.edu/software/scan-upc/

Also, if you are still worried about batch effects, I have already solved the batch/confounding problem. I now have a ComBat script that can adjust for Batch Effects in confounded designs. However, I have not published this work yet. I'm working on the manuscript now and hope to have it published within a few months, therefore: 
	a. You can wait for the publication and then use the ComBat for confounded variables. 
	b. Alternatively, I can help you adjust your data using my beta version of my confounded ComBat, but I have a policy to not release my unpublished methods unless you are willing to include me as a collaborator on your manuscript (assuming that the confounded ComBat works well on your data). If you don't want to wait, send me a personal email and we can discuss options for collaboration and for getting your confounded data adjusted. 

Hope this helps. Thanks!

Evan

--
W. Evan Johnson, PhD
Assistant Professor of Medicine
Division of Computational Biomedicine
Boston University Department of Medicine
72 East Concord St., E-645
Boston, MA 02118



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