[BioC] SE using RMA

Rafael A. Irizarry ririzarr at jhsph.edu
Tue Apr 8 12:07:16 MEST 2003

a) if you use expresso instead of the rma funciton i believe you get 
ad-hoc se estimtates. to extract them from the exprSet use the method 
se.exprs(). ben bolstad is working on improving the se estimate. basically 
by using rlm instead of the current ad-hoc procedure.

b) not a concrete one. coding up what Affymetrix does is straight forward 

c) to the best of my knowledge, there wont be many differences between 
this release and the next. 

On Tue, 8 Apr 2003, Christian M. Probst wrote:

> Hi,
> I am using the RMA function to analyze Genechip arrays.
> I would like to know if:
> a) There is an option to calculate the SE for the expression summary?
> b) There is any plan to add a statistical test of gene status as in MAS 5.0
> (absent, present) using the background correct and only PM data.
> c) What are the main implementations in Affy 1.2.9?
> Thanks in Advance
> Christian
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