[BioC] More iterations for median polish using Expresso

[Martin Morgan]

Hi James, James,

I think the summary.param parameter does this, e.g., going in the other 
direction...

example(expresso)

expresso(Dilution, bgcorrect.method="rma", normalize.method="constant", 
pmcorrect.method="pmonly", summary.method="medianpolish", 
summary.param=list(maxiter=1))

James W. MacDonald wrote:
> 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:

a 'warning', not an error.

Martin

>>
>> 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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> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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