[BioC] Encountering error when using GOstats package

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Sep 25 21:04:59 CEST 2008

> Hi Vincent,
> Thanks for your reply.
> I uninstalled the non-SQLite package using:
>  > remove.packages('ath1121501')
> I then re-ran the code I posted.  Still got the error :-(
> (new sessionInfo also posted below)
> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>    variable "ath1121501ENTREZID" was not found
> Error in mget(probes, ID2EntrezID(datPkg)) :
>    error in evaluating the argument 'envir' in selecting a method for function

ok -- it seems that there are no Entrez Gene identifiers for
arabadopsis defined in the ath1121501.db -- use ath1121501()
to see what mappings are there.  i personally do not know whether
such mappings exist.  i believe you will have to be more specific
in your choice of the universe specification when creating the
GOHyperGParams object.  i do not see an org.* package for arabadop.

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