[BioC] rma and MM

[Justin Borevitz]

Justin
http://naturalvariation.org 

We are having a little debate about whether RMA is using MM oligos at all.
I know that PM.only is the method that calls the gene expression index, but
Are MM intensities used in the calculation for the background correction?  I
thought I'd put this out to get the definitive answer.

One that note, if they are used does it really help that much?  If people
are interested, I for 1 would be happy to hear thoughts (on or off line) on
whether MM oligos are worth the space for custom affy array designs.  With
the analysis we are doing now (RMA and probe level models) it seems to me
the answer is no.

Justin
http://naturalvariation.org