[BioC] how to update DEseq package on windows?

Nicolas Delhomme delhomme at embl.de
Wed Feb 15 17:38:32 CET 2012


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
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