[BioC] expresso ( medianpolish & pmcorrect="subtractmm") Issue

[Rafael A. Irizarry]

the affy package provides the infrastucture so that you can define 
whatever functions you want. for example, the function hlog (hybrid log) 
is included in the package. you can change easily write a function called 
mymedianpolish and use it instead of log2.

-rafael
 On Thu, 5 Dec 2002, Sundaram, Shyam 
(NIH/CIT) wrote:

> Hi:
> I thought I would like to share a situation that I have been facing. It is
> not a bug but something that happens in a specific condition. When you use
> the "medianpolish" method in "expresso" and also use the "subtractmm" option
> in the "pmcorrect" option you will find that the method will blow up. The
> reason for this is sometimes the PM-MM will yield "negative" values and this
> will cause the "NaN" values.
> 
> I guess is it good to have the ability to choose the transformation function
> to something other than log2 for negative values.
> 
> Any suggestions/thoughts on this.
> 
> Thanks
> Shyam
> 
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