[BioC] problem

[Wei.Hu@uchsc.edu]

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