[BioC] RMA and missing values

[Wenbin Liu]

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.

Any experienced users who encounter this problem?

Thanks a lot!

Wenbin