hello there, As R could not find "xlaevis2probe" in Bioconductor repository, I could not finish my Affymetrix GeneChip analysis by gcRMA. The file does not seem to exist neither on the repository, nor the bioconductor.org website. But the original affymetrix probe sequence file itself was available from affymetrix website. Does anyone know how to make the Probe sequence data for microarrays of type xenopuslaevis 2 ? Thank you Asurain error message was as follows: [1] "Environment xlaevis2probe was not found in the Bioconductor repository." Error in get(probepackagename) : variable 'xlaevis2probe' was not found.

Hi Asurain, Naoki Irie wrote: > hello there, > > > As R could not find "xlaevis2probe" in Bioconductor repository, I could not > finish my Affymetrix GeneChip analysis by gcRMA. > The file does not seem to exist neither on the repository, nor the bioconductor.org website. > > But the original affymetrix probe sequence file itself was available from affymetrix website. > > Does anyone know how to make the Probe sequence data for microarrays of type xenopuslaevis 2 ? This was an oversight on my part, and the package will be included in the next release of Bioconductor (coming up in 8 weeks or so). To build a probe package yourself, you use the tab-delimited probe file from Affymetrix along with the makeProbePackage() function from AnnotationDbi. This will create a folder in your current working directory that can be built and installed using the R package building system (R CMD build and R CMD INSTALL). If you are on linux, you should be able to do these things by default. If on Windows, you will need to get the Rtools toolset that Duncan Murdoch makes available on his page: http://www.murdoch-sutherland.com/Rtools/ If on MacOS, you will need to get the Xcode toolset and the GNU Fortran compiler from this page: http://r.research.att.com/tools/ I have sent you the source and Windows binary offline, so hopefully either of those will work for you. If you are on a Mac, then you will first need to get the tools from above. Best, Jim > > Thank you > > Asurain > > > error message was as follows: > > [1] "Environment xlaevis2probe was not found in the Bioconductor repository." > Error in get(probepackagename) : > variable 'xlaevis2probe' was not found. > > _______________________________________________ > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues