[BioC] Hg18 build of org.Hs.eg.db

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Sep 21 18:16:10 CEST 2010


On Tue, Sep 21, 2010 at 12:09 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> I believe the best way would be to install the "release" version of R
> that coincides with the org.Hs.eg.db
> version that you are interested in, and install it into that version
> of R with biocLite.  In my lab we have
> simultaneous availability of R 2.10, 2.11, and 2.12 (and now 2.13) to
> allow continuity of ongoing analyses.
> The user must pick the appropriate version.

While this generally works, it's somehow non optimal for this
particular problem especially because the package in question is an
annotation package.

Consider the situation where the user wants to use Rsamtools (not
available in R 2.10) but is performing analyses against hg18.

One could argue that perhaps the GenomicFeatures package would be
better suited to replace the genome-version-specific info I'm guessing
the OP wanted from org.Hs.eg.db, but I'm just giving an example.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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