[BioC] RMA values for Affy Mouse Exon array

[James W. MacDonald]

Hi Peter,

Peter Saffrey wrote:
> I've had success in the past using the affy package on human affy gene 
> arrays. However, I can't seem to get the CDF environment setup properly.
> 
> I've installed the Mouse Exon CDF from here:
> 
> http://xmap.picr.man.ac.uk/download/#mmcdf
> 
> but I'm not quite clear about the second instruction to "attach the CDF 
> to the AffyBatch object". Can anybody fill me in?

data at cdfName <- "mouseexonpmcdf"

Note that data isn't a really good variable name, as that is a name of a 
function as well. R is actually very good about distinguishing between 
the two, but I generally try not to mask functions with variable names.

Best,

Jim


> 
> Sorry if this is a stupid question - I am quite new to BioConductor and 
> still mostly at the copy-and-paste-and-hope stage... I've pasted my 
> session at the bottom of this message.
> 
> Thanks,
> 
> Peter
> 
> 
> 
> 
>  > library("affy")
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
>  > library("mouseexonpmcdf")
>  > data <- ReadAffy()
>  > rma <- rma(data)
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoEx-1_0-st-v1
> Library - package moex10stv1cdf not installed
> Bioconductor - moex10stv1cdf not available
>  > sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-pc-linux-gnu
> 
> locale:
> C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
> 
> other attached packages:
> [1] mouseexonpmcdf_1.1 affy_1.20.2        Biobase_2.2.2
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        preprocessCore_1.4.0
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826