Hello, everyone I am currently analyzing 3 SNP arrays of type Affymetrix Mouse Diversity Genotyping Array. Unfortunately there is no CDF environment or annotation package available yet. So I tried to build an CDF environment on my own using make.cdf.env() function and the CDF file provided by Affymetrix library files. Calling > MOUSEDIVm520650 <- make.cdf.env("SNPchipdata/AffyChipAnnot/MOUSEDIVm520650.CDF") I got the error message : "makecdfenv does not currently know how to handle cdf files of this type (ie not expression or genotyping)" > traceback() 2: .Call("ReadCDFFile", file.path(path.expand(cdf.path), filename), PACKAGE = "affyio") 1: make.cdf.env("SNPchipdata/AffyChipAnnot/MOUSEDIVm520650.CDF") When I searched the internet for this error, I found an older message in this mailing list (http://bit.ly/fAYxOM), where it was mentioned, that "make.cdf.env is for 3' biased gene expression arrays only, really.". So my question is, if anybody of you could tell me how to deal with that problem or CDF file? I can't imagine, that I am the first guy facing that problem with this type of arry here? I tried R 2.10.* (bioconductor 2.5) and R 2.12 (bioconductor 2.7), but I had always the same problems. My sessionInfo() is R version 2.10.1 (2009-12-14) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks for your help! Best regards, Christoph

Hi Christoph, On 12/14/2010 5:31 AM, Christoph Standfu? wrote: > Hello, everyone > > I am currently analyzing 3 SNP arrays of type Affymetrix Mouse Diversity > Genotyping Array. Unfortunately there is no CDF environment or > annotation package available yet. So I tried to build an CDF environment > on my own using make.cdf.env() function and the CDF file provided by > Affymetrix library files. > > Calling > > > MOUSEDIVm520650 <- > make.cdf.env("SNPchipdata/AffyChipAnnot/MOUSEDIVm520650.CDF") > > I got the error message : "makecdfenv does not currently know how to > handle cdf files of this type (ie not expression or genotyping)" > > > traceback() > 2: .Call("ReadCDFFile", file.path(path.expand(cdf.path), filename), > PACKAGE = "affyio") > 1: make.cdf.env("SNPchipdata/AffyChipAnnot/MOUSEDIVm520650.CDF") > > > When I searched the internet for this error, I found an older message in > this mailing list (http://bit.ly/fAYxOM), where it was mentioned, that > "make.cdf.env is for 3' biased gene expression arrays only, really.". > > So my question is, if anybody of you could tell me how to deal with that > problem or CDF file? I can't imagine, that I am the first guy facing > that problem with this type of arry here? You want to use the oligo package for this chip type. Best, Jim > > > > I tried R 2.10.* (bioconductor 2.5) and R 2.12 (bioconductor 2.7), but I > had always the same problems. > > My sessionInfo() is > > R version 2.10.1 (2009-12-14) > i686-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > Thanks for your help! > > Best regards, > > Christoph > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues