[BioC] limma - NA values after withinarray normalization

Gordon K Smyth smyth at wehi.EDU.AU
Sat Aug 4 09:23:09 CEST 2012

It has nothing to do with the normalization method.  See


and the bc.method argument to normalizeWithinArrays.


> Date: Thu, 2 Aug 2012 13:42:53 -0500
> From: "Zhang, Xueqiong" <xueqiong.zhang at Vanderbilt.Edu>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] limma - NA values after withinarray normalization
> Hi There,

>  I am using normalizeWithinArrays function from the limma package for a 
> within array normalization . There were no missing/NA values in the 
> input data file, however, after the within array normalization, there 
> are some of NA values in the M file , I wonder under which condition the 
> function returns NA to M ? How can I do a between array normalization 
> based on the within array normalized data which has some NA values?

>  FYI - My data is aCGH data from Agilent, the normalization method I 
> used was loess .
> thank you very much!
> I am looking forward to hearing back from you!
> Joan Zhang

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