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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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