[BioC] subtractmm problem in "affy"

Ben Bolstad bolstad at stat.berkeley.edu
Wed Apr 21 22:55:12 CEST 2004

the problem is that the medianpolish summarization method takes a log2
transformation of the data. if you use subtractmm  there is the
possibility of gettting negatives. Perhaps you want to use


which will used a modified version of MM. This will not give you the
same problem of NA.

On Wed, 2004-04-21 at 13:49, PARK,CHRISTOPHER CHANGSUN wrote:
> Hi all,
> I am trying to normalize microarray data using the subtractmm method using
> the "affy" library.
> The following is my R script:
> set.seed(123)
> library(affy)
> Data <- ReadAffy()
> eset<-expresso(Data,bgcorrect.method="rma",
> normalize.method="quantiles",
> pmcorrect.method="subtractmm",
> summary.method="medianpolish")
> write.exprs(eset,file="subtractmm_data.txt")
> During the normalization, I encounter the following error message:
> Error in if (converged) break : missing value where TRUE/FALSE needed
> In addition: Warning message: 
> NaNs produced in: log(x, base) 
> ...
> The processed data is a grid of NA's.
> Does anyone know what might be wrong here and what I could do to fix it?
> Thanks again for your help,
> Chris
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Ben Bolstad <bolstad at stat.berkeley.edu>

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