[BioC] NaNs in RMA normalization of GSE31312

[Anders Ellern Bilgrau [guest]]

Dear Bioconductor mailing list

I am trying to RMA normalize the GSE31312 gene expression dataset (from the Gene Expression Omnibus website) using the affy-package with and without custom Brainarray CDF annotations. However, the expression matrix are returned are filled with NaNs.

As I have not received any answers on stackoverflow.com, it was suggested to me that I cross-post the issue here:

http://stackoverflow.com/questions/23512911/all-nans-in-rma-normalization-of-gse31312-using-brainarray-custom-cdfs

Long story short. 
RMA normalization with standard CDFs yield 12305 NaNs in the expression matrix.
RMA normalization with Brainarray CDFs yield an expression matrix consisting of only NaNs. 
Removing the sample "GSM776462.CEL" removes all NaN problems in the Brainarray case, but not with the standard CDF.

Can anybody help me to shed some light on the origin of these NaNs?

Many thanks for any help!
Anders E Bilgrau

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] R.utils_1.29.8       R.oo_1.18.0          R.methodsS3_1.6.1    affy_1.42.2         
[5] GEOquery_2.30.0      Biobase_2.24.0       BiocGenerics_0.10.0  BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] affyio_1.32.0         preprocessCore_1.26.1 RCurl_1.95-4.1        tools_3.1.0          
[5] XML_3.98-1.1          zlibbioc_1.10.0      

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