H i there I am reading cel files from genechip miRNA 2.0 array affymatrix in to affy package spleen.affy = ReadAffy() for gcrma I get >gcrma(spleen.affy) I get following error [1] "Environment mirna20probe was not found in the Error in get(probepackagename) : object 'mirna20probe' not found where do I get that 'mirna20probe package Thanks -- output of sessionInfo(): > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Ireland.1252 LC_CTYPE=English_Ireland.1252 LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C [5] LC_TIME=English_Ireland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationDbi_1.14.1 limma_3.8.3 gcrma_2.24.1 puma_2.4.0 mclust_3.4.10 mirna20cdf_2.8.0 affy_1.30.0 [8] Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 Biostrings_2.20.3 DBI_0.2-5 IRanges_1.10.6 preprocessCore_1.14.0 RSQLite_0.10.0 splines_2.13.1 [8] tools_2.13.1 > -- Sent via the guest posting facility at bioconductor.org.

As far as I know, Affy has never released a probe file for this array, so we don't have a probe package. Best, Jim On 10/19/2011 4:38 PM, ATTIA [guest] wrote: > H i there > I am reading cel files from genechip miRNA 2.0 array affymatrix in to affy package > spleen.affy = ReadAffy() > > for gcrma I get > >> gcrma(spleen.affy) > I get following error > [1] "Environment mirna20probe was not found in the > Error in get(probepackagename) : object 'mirna20probe' not found > where do I get that 'mirna20probe package > Thanks > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_Ireland.1252 LC_CTYPE=English_Ireland.1252 LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C > [5] LC_TIME=English_Ireland.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AnnotationDbi_1.14.1 limma_3.8.3 gcrma_2.24.1 puma_2.4.0 mclust_3.4.10 mirna20cdf_2.8.0 affy_1.30.0 > [8] Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 Biostrings_2.20.3 DBI_0.2-5 IRanges_1.10.6 preprocessCore_1.14.0 RSQLite_0.10.0 splines_2.13.1 > [8] tools_2.13.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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