Hello, I have been trying to use the package *[pd.mapping250k.sty]*, but I’m might be missing something. This is my procedure: > myData <- ReadAffy() > myData@cdfName [1] "Mapping250K_Sty" The CEL fled are loaded okay!! Then we proceed with the normalization procedure, and this is where the problem is: > eset <- rma(myData) *Error in getCdfInfo(object) :* * Could not obtain CDF environment, problems encountered: Specified environment does not contain Mapping250K_Sty* *Library - package mapping250kstycdf not installed* *Bioconductor - mapping250kstycdf not available* Then, I tried installing it: > biocLite(‘pd.mapping250k.sty’) > library(‘pd.mapping250k.sty’) The package installs okay (it is a ~350Mb package), and it DOES load properly, but when I tried to run rma(myData) again I get the same problem as above: *Error in getCdfInfo(object) :* * Could not obtain CDF environment, problems encountered: Specified environment does not contain Mapping250K_Sty* *Library - package mapping250kstycdf not installed* *Bioconductor - mapping250kstycdf not available* I CAN rma normalize other CEL files using hgu133plus2cdf, or hgu133acdf, but NOT with Mapping250K_Sty. Any suggestions? Thanks, Marcelo [[alternative HTML version deleted]]

Hi Marcelo, For SNP chips of that type, you want to use the oligo package, and the crlmm function. Best, Jim On Aug 8, 2014 3:23 PM, "Marcelo Pereira" <marcelops@gmail.com> wrote: > Hello, > > I have been trying to use the package *[pd.mapping250k.sty]*, but I’m might > be missing something. > > This is my procedure: > > > myData <- ReadAffy() > > myData@cdfName > > [1] "Mapping250K_Sty" > > > The CEL fled are loaded okay!! Then we proceed with the normalization > procedure, and this is where the problem is: > > > eset <- rma(myData) > > *Error in getCdfInfo(object) :* > * Could not obtain CDF environment, problems encountered: Specified > environment does not contain Mapping250K_Sty* > *Library - package mapping250kstycdf not installed* > *Bioconductor - mapping250kstycdf not available* > > > Then, I tried installing it: > > > biocLite(‘pd.mapping250k.sty’) > > library(‘pd.mapping250k.sty’) > > The package installs okay (it is a ~350Mb package), and it DOES load > properly, but when I tried to run rma(myData) again I get the same problem > as above: > > *Error in getCdfInfo(object) :* > * Could not obtain CDF environment, problems encountered: > Specified environment does not contain Mapping250K_Sty* > *Library - package mapping250kstycdf not installed* > *Bioconductor - mapping250kstycdf not available* > > > I CAN rma normalize other CEL files using hgu133plus2cdf, or hgu133acdf, > but NOT with Mapping250K_Sty. > > Any suggestions? > > Thanks, > Marcelo > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]