[BioC] Missing Values after cyclic loess in limma

[Claus Mayer [guest]]

Hello,

I am just working on my first ever single channel Agilent array data set. Because I do expect large changes in differential expression I wanted to use the cyclic loess normalisation within limma rather than quantile normalisation. I used the default settings i.e. 

y<-normalizeBetweenArrays(x,method="cyclicloess")

where x is the ELlistRaw object. As expected this took a while but to my surprise produced hundreds of missing values for each array as indicated by the message

Warning message:
In log2(Recall(object$E, method = method, ...)) : NaNs produced

I checked the raw values which are all well above 0 and include no NAs. I also did not use any background correction, so I don't quite understand why logging should produce any missing values. I had assumed that the method would first log and then apply the cyclic loess algorithm, which in itself shouldn't produce any NAs either. Have I misunderstood something basic here?

Thanks,

Claus



 -- output of sessionInfo(): 

R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)

other attached packages:
[1] limma_3.8.2    

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