[BioC] problem

[Laurent Gautier]

On Mon, Jan 20, 2003 at 09:35:29PM -0700, 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.

The 'rma' was supposed to be a streamlined version in C of the second one.
It was included as such few days before the release. It appears that the
results differ because the code differs (which is I think is both a problem
and should have been stated in the documentation.) Sorry for that. 

>  
> 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:  


The warnings are only stating that something caused trouble (in this case
there is no convergence). You may want to take note of these genes and
be extra-careful with them in your analysis.
I just saw that a part of the warning/error handling stuff did not make
it to the release. You may try the following if the warnings cause you trouble:

options(show.error.messages = FALSE)
eset<-expresso(affybatch, normalize.method="invariantset", bg.correct=F, pmcorrect.method="pmonly", summary.method="liwong", warnings=FALSE)


Hopin' it helps,


Laurent


> 
> 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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