When I run gcrma I get > AB_gcrmaNumhom2 <- gcrma(AA_ReadAffyNumhom, fast = FALSE) Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .9 Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .9 trying URL 'http://bioconductor.org/packages/2.4/data/annotation/bin/macosx/leopa rd/con trib/2.9/porcinecdf_2.4.0.tgz' Content type 'application/x-gzip' length 1879945 bytes (1.8 Mb) opened URL ================================================== downloaded 1.8 Mb If I try to go to <http: brainarray.mbni.med.umich.edu="" bioc="" bin="" macosx="" leopard=""> Safari say "page cannot be found" Ignore this? Or do I now have a problem? ======================================= > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] porcineprobe_2.4.0 AnnotationDbi_1.6.0 porcinecdf_2.4.0 gcrma_2.16.0 Biostrings_2.12.1 IRanges_1.2.0 [7] affy_1.22.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 RSQLite_0.7-1 splines_2.9.0 [6] tools_2.9.0 =================== Thank you

Loren Engrav wrote: > When I run gcrma I get > >> AB_gcrmaNumhom2 <- gcrma(AA_ReadAffyNumhom, fast = FALSE) > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.9 > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.9 > trying URL > 'http://bioconductor.org/packages/2.4/data/annotation/bin/macosx/leo pard/con > trib/2.9/porcinecdf_2.4.0.tgz' > Content type 'application/x-gzip' length 1879945 bytes (1.8 Mb) > opened URL > ================================================== > downloaded 1.8 Mb > > If I try to go to > <http: brainarray.mbni.med.umich.edu="" bioc="" bin="" macosx="" leopard=""> > Safari say "page cannot be found" > > Ignore this? Or do I now have a problem? Ignore it, unless you want to use MBNI packages (which it seems you do not want to do). Best, Jim > > ======================================= >> sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-apple-darwin9.6.0 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] porcineprobe_2.4.0 AnnotationDbi_1.6.0 porcinecdf_2.4.0 gcrma_2.16.0 > Biostrings_2.12.1 IRanges_1.2.0 > [7] affy_1.22.0 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0 > RSQLite_0.7-1 splines_2.9.0 > [6] tools_2.9.0 > =================== > > Thank you > > _______________________________________________ > 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