[BioC] problem

[Rafael A. Irizarry]

hi!

the method RMA is constantly being improved. the affy package function 
"rma" will reflect these changes, so expect to see different versions 
in future release.  
for now, expresso, as you called it, 
will give you the original version of RMA. there is a 
subsection in the vignette entitled "C implementation of RMA" that 
contains more information (and in the future better documentation).

rafael



 On Mon, 20 Jan 2003 
Wei.Hu@uchsc.edu wrote:

> Hi, everyone:
>         I have some problems with affy package in bioconductor.I ran both
> eset<-rma(affybatch) and eset<- expresso(affybatch,
> normalize.method="quantiles", bg.method="rma",
> pmcorrect.method="rma",summary.method="medianpolish") 
> The results are different. The former seemed to run much faster.
>  
> I also rarn dchip. eset<-expresso(affybatch,
> normalize.method="invariantset", bg.correct=F, pmcorrect.method="pmonly",
> summary.method="liwong") I have 2 groups and each group has 19 samples.
> The result came out finally, but with some warnings like the following:  
> 
> 1: No convergence in inner loop after 50 in outerler tieration 1 
> 
>  in: fit.li.wong(probes, ...) 
> 
> 2: No convergence achieved in outlier loop
> 
>  in: fit.li.wong(probes, ...) 
> 
> 3: No convergence achieved in outlier loop
> 
>  in: fit.li.wong(probes, ...) 
> 
> 4: No convergence in inner loop after 50 in outerler tieration 1 
> 
>  in: fit.li.wong(probes, ...) 
> 
> 5: No convergence in inner loop after 50 in outerler tieration 1 
> 
>  in: fit.li.wong(probes, ...) 
> 
> 6: No convergence in inner loop after 50 in outerler tieration 1 
> 
>  in: fit.li.wong(probes, ...) 
> 
> 7: No convergence in inner loop after 50 in outerler tieration 1 
> 
>  in: fit.li.wong(probes, ...) 
> 
> 8: No convergence achieved in outlier loop
> 
>  in: fit.li.wong(probes, ...) 
> 
> 9: No convergence achieved in outlier loop
> 
>  in: fit.li.wong(probes, ...) 
> 
> 10: No convergence in inner loop after 50 in outerler tieration 1 
> 
>  in: fit.li.wong(probes, ...)  
> 
>  Thanks a lot
> 
> Wei
> 
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