[BioC] Kegg pathway --> gene network

[Martin Morgan]

Elliot Kleiman <kleiman at rohan.sdsu.edu> writes:

> Hi Fraser,
>
> Although KEGGgraph has not yet been
> formally released, you may still manually
> install it.

This sounds like a very dangerous solution -- packages have
complicated and often implicit dependencies. This will, sooner or
later, lead to grief -- an obscure error caused by incompatibilities
between packages from different release versions. A non-negligible
fraction of the mail on this list is from exactly this situation. The
'what is your sessionInfo()' / 'update your packages' solution that
most often addresses the problem takes time away from more meaningful
work, for all parties. Might as well just 'do it right' in the first
place.

Martin

> First, download it to your local machine
> * [ http://www.bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html ]
>
> For example, I am [still] running R version 2.7.2 and I have installed
> KEGGgraph, by doing, ...
>
> # must be su (or root) or have sudo permissions
> % R CMD INSTALL KEGGgraph_0.8.7.tar.gz
>
> # print-out sessionInfo()
>  > sessionInfo()
> R version 2.7.2 (2008-08-25)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] RBGL_1.18.0      biomaRt_1.14.1   RCurl_0.92-0     Rgraphviz_1.18.1
> [5] KEGGgraph_0.8.7  graph_1.20.0     XML_1.98-1
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11 tools_2.7.2
>
> Hope that helps,
>
> ... Elliot
>
> -- 
> MS graduate student Computational Science Program San Diego State
> University
> http://www.csrc.sdsu.edu/ http://www.sdsu.edu/
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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