[BioC] RE: Bioconductor digest, Vol 1 #208 - 2 msgs

[Rafael A. Irizarry]

the function fit.li.wong operates on a matrix representing a probe 
set and returns a list. there are two components having to 
do with convergence: convergence1 (algorithm didnt converge after maxit 
iterations) and convergence2 (too many outliers). expresso does not return 
these but it shouldnt be too hard to tweak.

hope this helps,
rafael
On Tue, 21 Jan 2003, Aaron Aragaki wrote:

> Howdy
> 
> I have a question stemming from Laurent's response to Wei's question (21Jan03). 
> 
> Here's a quick recap:
> 
> WEI'S PROBLEM:  He gets convergence warnings when performing a dchip normalization.
> eset<-expresso(affybatch,normalize.method="invariantset", bg.correct=F, pmcorrect.method="pmonly",summary.method="liwong") 
> 1: No convergence in inner loop after 50 in outer .............
> 
> LAURENT'S RESPONSE:
> "You may want to take note of these genes and be extra-careful with them in your analysis."
> 
> MY QUESTION:
> How do I extract the names of genes that are associated with the non-convergence?
> i.e., Is there a function that will produce a list of gene (that i need to be "extra-careful with") from the expresso object, eset?
> 
> Thanks
> 
> Aaron
> 
> Aaron K. Aragaki 		
> Statistical Research Associate
> Women's Health Initiative, Fred Hutchinson Cancer Research Center
> 206-667-6734
>      fax:  4142
> 
> http://www.whi.org
> http://www.fhcrc.org
> 
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