Good to hear about the RefPlus package, as that will be extremely useful.

We published a paper a couple of months ago that looks at performance of a 
"reference RMA" model built using a reference database of.cel files from 
samples of multiple tissues vs. the classic RMA workflow based on 
single-organ .cel files.

It is freely available here:  http://www.biomedcentral.com/1471-2105/7/464

Mark

Mark Porter
Director, Biostatistics and Data Analysis
Gene Logic Inc.
50 West Watkins Mill Rd.
Gaithersburg MD  20879
Phone: 240/364-7638
Fax: 240/364-7604
Email: mporter@genelogic.com

Mailing Address/Corporate Headquarters:
610 Professional Drive
Gaithersburg, MD 20879



Hi James,

Can I point you in the direction of the RefPlus package available in
Bioconductor release 2.0, which will do what I think you are looking
for, i.e. allowing additional cel files to be added into a data set
without affecting the gene expression or the normalisation parameters
calculated from the previously processed cel files. 

You might also want to check out the paper from Darlene Goldstein in
Bioinformatics (2006 p2364-2372) which discusses similar algorithms.

All the best

Chris

Chris Harbron
Technical Lead Statistician,
AstraZeneca

 

	[[alternative HTML version deleted]]

