[BioC] ERCC spike-in probes in

Brian Abraham [guest] guest at bioconductor.org
Mon Jun 24 21:33:11 CEST 2013

Hi team,

I'm part of the lab that made everyone's microarray analysis more difficult by demanding everyone do ERCC spike-in normalization.  Unfortunately, the primeviewcdf does not automatically contain the probeset IDs for ERCCs, despite the probes being physically on the chip.  We've worked with Affy to get a custom cdf made that contains the locations of the ERCC probes on the primeview chip.  Would you be interested in folding this into your code so that more people can benefit from it?

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] makecdfenv_1.36.0  affyio_1.28.0      affy_1.38.1        Biobase_2.20.0    
[5] BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] BiocInstaller_1.10.2  preprocessCore_1.22.0 tools_3.0.1          
[4] zlibbioc_1.6.0 

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