[BioC] question of medianpolish in RMA

[James W. MacDonald]

Simon Lin wrote:
> How can the medianpolish used in RMA ensure that
> both
>   alpha (probe affinity) and beta (expression abundance)
> larger than zero?
> 
> Or, RMA occasionally gives out negative expression values?

Medianpolish is run on log transformed values, so if by chance there 
were a bunch of data in the range (0 - 1) before taking logs, it is 
possible that some of the expression values could be negative. However, 
I have analyzed hundreds of chips and have yet to see a negative value, 
so I think the likelihood of such a thing happening is remote.

Best,

Jim


> 
> Thanks!
> 
> Simon
> 
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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
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