I am using R 2.12.1 and I would like to use the new function estimateDispersions() of from DESeq package 1.4.1.
The problem I am facing is that I am running the version 1.2.1 of DESeq but cannot update to the last version ... Typically, to update I use:
but that doesnt work ... I read somewhere that I need r-dev to make it work, it is installed but that doesnt change a thing.
Any help is appreciated. Thanks
R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=C LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  DESeq_1.2.1 locfit_1.5-6 lattice_0.19-13 akima_0.5-4  Biobase_2.10.0 loaded via a namespace (and not attached):  annotate_1.28.1 AnnotationDbi_1.12.1 DBI_0.2-5  genefilter_1.32.0 geneplotter_1.28.0 grid_2.12.1  RColorBrewer_1.0-5 RSQLite_0.9-4 splines_2.12.1  survival_2.36-2 tools_2.12.1 xtable_1.5-6
EDIT: I tried to manually install DESeq 1.4.1 but I get this error:
Error : package 'Biobase' 2.10.0 was found, but >= 2.13.6 is required by 'DESeq' ERROR: lazy loading failed for package ‘DESeq’
but I cannot find BioBase 2.13.6 anywhere :(