[BioC] More iterations for median polish using Expresso

James W. MacDonald jmacdon at med.umich.edu
Mon Jun 1 22:57:09 CEST 2009


Hi James,

jchayes at mcb.umass.edu wrote:
> My name is James and I am having trouble normalizing some microarray data.  I
> have three microarray sets that I am trying to normalize using expresso.  Here
> is what I type and the error message which follows:
> 
> cphy.prenorm <- expresso(cphy.data, bgcorrect.method="rma",
> + normalize=FALSE,pmcorrect.method="pmonly",
> + summary.method="medianpolish")
> background correction: rma
> PM/MM correction : pmonly
> expression values: medianpolish
> background correcting...done.
> 11092 ids to be processed
> |                    |
> |####################|
> Warning message:
> In medpolish(log2(x), trace.iter = FALSE, ...) :
>   medpolish() did not converge in 10 iterations
> 
> Can I increase the number of iterations in expresso or do I have to do each step
> one at a time?  Any help you can give me would be greatly appreciated.

Not easily. If you really want to do this, you can download the sources 
and then modify the generateExprVal.method.medianpolish() function, 
adding a maxiter=30 or whatever, and then build and install the package.

Best,

Jim




> 
> Best Regards,
> 
> James
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826



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