my DEseq package could not find the estimateDispersions( ) function but it can find the old function estimateVarianceFunctions(cds) i donot know how to update this package > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq_1.4.1 locfit_1.5-6 lattice_0.19-30 akima_0.5-7 Biobase_2.12.2 loaded via a namespace (and not attached): [1] annotate_1.30.1 AnnotationDbi_1.14.1 DBI_0.2-5 genefilter_1.34.0 geneplotter_1.30.0 [6] grid_2.13.1 RColorBrewer_1.0-5 RSQLite_0.10.0 splines_2.13.1 survival_2.36-9 [11] tools_2.13.1 xtable_1.5-6 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

Fetching the latest stable version of R (2.14.1) would solve that issue. You would then have access to Bioconductor version 2.9 and every updated stable package. If you're more adventurous you could get the latest development version (R-2.15) and get access to the daily updated Bioconductor version 2.10 packages. In a nutshell, every 6 month a new R version is released and so are new matching bioconductor versions. As you can realize from the examples above, they always go in pair :-) Trying to use recent bioconductor package with an older R version is definitely the last thing you want to do. Cheers, --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 15 Feb 2012, at 17:11, wang peter wrote: > my DEseq package could not find the > estimateDispersions( ) function > but it can find the old function > estimateVarianceFunctions(cds) > > i donot know how to update this package > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DESeq_1.4.1 locfit_1.5-6 lattice_0.19-30 akima_0.5-7 > Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] annotate_1.30.1 AnnotationDbi_1.14.1 DBI_0.2-5 > genefilter_1.34.0 geneplotter_1.30.0 > [6] grid_2.13.1 RColorBrewer_1.0-5 RSQLite_0.10.0 > splines_2.13.1 survival_2.36-9 > [11] tools_2.13.1 xtable_1.5-6 > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu > Facebook:http://www.facebook.com/profile.php?id=100001986532253 > > _______________________________________________ > 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