[BioC] RMA and missing values

[James W. MacDonald]

Wenbin Liu wrote:
> Hi there!
> 
> I used function rma() in the affy package (devel ver.
> 1.5.6) to normalized an AffyBatch that has missing
> values. The function density() in the body of rma()
> gives an error. I changed the na.rm=FALSE to TRUE, and
> the program was quiet. However, the result (of class
> ExprSet) got many more probe sets with NA values than
> the AffyBatch originally had. 
> 
> This is rather undesirable because a minor to moderate
> masking of the probe intensity values will cause the
> loss of a large number of probe sets.

Why exactly are you masking probes? This is something that even 
Affymetrix says is rarely used ("Masks are rarely used features in MAS. 
"). Given the robust model fit used in RMA, I can't think of a good 
reason to exclude probe intensity values.

Jim


> 
> Any experienced users who encounter this problem?
> 
> Thanks a lot!
> 
> Wenbin
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109