[BioC] MGU74A and MGU74Av2

[David O. Nelson]

On Fri, 2003-06-20 at 11:24, Yongde Bao wrote:
> David:
> 
> Can you tell us how you dealt with the masked genes in MG 74A with rma?
> 

I didn't. As I understand RMA (please correct me if I'm wrong here), the
default approach is to use Ben Bolstad's quantile normalization followed
by a robust fit of an additive model (y ~ array + probe) to each probe
set separately.

So, if you confine your attention to one chip type for your arrays, the
normalization should go thru OK, and the fact that a particular probe
set is spectacularly bad in predicting expression levels doesn't affect
the expression estimates for other probe sets.
 
Is that line of reasoning bogus?

dave


> Thanks, Yongde Bao


-- 
David O. Nelson <daven at llnl.gov>
LLNL