Dear R experts and / or DESeq expert(s),
I am using DESeq v1.8.2 and would like to upgrade. The current version available is v1.9.4.
From an R session, I am using the update.packages() command .. (please see below for details), but it does not work.
Q1- Can you please suggest a fix. Which R command / series of commands would work?
Q2 - Would this be a general fix for upgrading to other such R packages, such as edgeR.
Thanks in advance.
Best,
sarosh
I am using DESeq v1.8.2 and would like to upgrade. The current version available is v1.9.4.
From an R session, I am using the update.packages() command .. (please see below for details), but it does not work.
Q1- Can you please suggest a fix. Which R command / series of commands would work?
Q2 - Would this be a general fix for upgrading to other such R packages, such as edgeR.
Thanks in advance.
Best,
sarosh
Code:
> require(DESeq); > sessionInfo(); R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.4 DESeq_1.8.2 locfit_1.5-8 [4] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] annotate_1.34.0 AnnotationDbi_1.18.0 DBI_0.2-5 [4] genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0 [7] IRanges_1.14.2 lattice_0.20-6 RColorBrewer_1.0-5 [10] RSQLite_0.11.1 splines_2.15.0 stats4_2.15.0 [13] survival_2.36-14 tcltk_2.15.0 tools_2.15.0 [16] xtable_1.7-0 > -------------------------------------------------------------- > update.packages("DESeq"); > -------------------------------------------------------------- -------------------------------------------------------------- > sessionInfo(); R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.4 DESeq_1.8.2 locfit_1.5-8 [4] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] annotate_1.34.0 AnnotationDbi_1.18.0 DBI_0.2-5 [4] genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0 [7] IRanges_1.14.2 lattice_0.20-6 RColorBrewer_1.0-5 [10] RSQLite_0.11.1 splines_2.15.0 stats4_2.15.0 [13] survival_2.36-14 tcltk_2.15.0 tools_2.15.0 [16] xtable_1.7-0 --------------------------------------------------------------
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