[BioC] Missing Values after cyclic loess in limma

[Gordon K Smyth]

Dear Claus,

You are using software that is three Bioconductor releases out of date.

The bug you have run into was fixed on 5 August 2011.

Please install the current versions of R and Bioconductor.  See the 
posting guide:

  http://www.bioconductor.org/help/mailing-list/posting-guide/

Best wishes
Gordon

> Date: Fri,  2 Nov 2012 10:45:17 -0700 (PDT)
> From: "Claus Mayer [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, claus at bioss.ac.uk
> Subject: [BioC] Missing Values after cyclic loess in limma
>
>
> 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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