[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
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
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>
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