[BioC] RMA values for Affy Mouse Exon array

Peter Saffrey pzs at dcs.gla.ac.uk
Fri Aug 28 17:54:29 CEST 2009


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?

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



More information about the Bioconductor mailing list