[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

[mcarlson at fhcrc.org]

Source files should be up for these packages now.  Windows zip files should
follow very soon.

    Marc

Quoting Herve Pages <hpages at fhcrc.org>:

> Hi Jenny,
> 
> We've fixed the problem you reported earlier with the ACCNUM map for
> arabidopsis.
> The new ag and ath1121501 packages will be online soon (we will post again
> when
> they are).
> 
> Sorry that my temporary workaround was producing a list instead of an
> environment
> and thanks to Jim and Martin for providing a quick solution to the problem.
> 
> Let me add a couple of comments related to this issue:
> 
>  - If you use the ath1121501.db package (the SQLite-based versions of
> ath1121501),
>    then you'll be able to use the fixed ACCNUM map right now (don't forget to
> use
>    the latest version of AnnotationDbi though). The most visible difference
> between
>    our new SQLite-based metadata packages and our classic environment-based
> metadata
>    packages is that the maps in the formers are S4 objects (AnnDbBimap
> objects to
>    be precise) instead of environments.
>    Don't be afraid by this: we've put a lot of effort to make those objects
> look
>    and feel like environments i.e. you can still use length, ls, mget,
> eapply, get,
>    [[, etc... on them.
>    hyperGTest() should work as expected with ath1121501.db. Please let us
> know if
>    this is not the case.
> 
>  - In the ath1121501.db package (and soon in the fixed version of the
> ath1121501
>    package), the ACCNUM and MULTIHIT maps are complementary: when a probe id
> is
>    mapped to a single AGI locus ID, then ath1121501MULTIHIT is set to NA:
> 
>      > library(ath1121501.db)
>      > ath1121501ACCNUM[["246779_at"]]
>      [1] "AT5G27520"
>      > ath1121501MULTIHIT[["246779_at"]]
>      [1] NA
> 
>    and when it's mapped to multiple AGI locus IDs, then ath1121501ACCNUM is
> set
>    to "multiple":
> 
>      > ath1121501ACCNUM[["264451_s_at"]]
>      [1] "multiple"
>      > ath1121501MULTIHIT[["264451_s_at"]]
>      [1] "AT1G10260" "AT1G11265" "AT1G21945" "AT1G48710" "AT1G58140"
> "AT3G32415"
>      [7] "AT3G59720" "AT3G61330" "AT5G13205"
> 
>    You can easily create a new map that contains the "merged" data from the
>    2 maps with:
> 
>      > ath1121501ALLACCNUMS <- as(ath1121501ACCNUM, "AnnDbBimap")
>      > ath1121501ALLACCNUMS[["246779_at"]]
>      [1] "AT5G27520"
>      > ath1121501ALLACCNUMS[["264451_s_at"]]
>      [1] "AT1G10260" "AT1G11265" "AT1G21945" "AT1G48710" "AT1G58140"
> "AT3G32415"
>      [7] "AT3G59720" "AT3G61330" "AT5G13205"
> 
>    This works with the SQLite-based annotations only (and it is very fast).
>    We will add some examples in the man page for those 2 maps to illustrate
>    this "merging" operation.
> 
> Cheers,
> H.
> 
> 
> Jenny Drnevich wrote:
> > Thanks Herve, Jim & Martin!
> > 
> > I've got it working now...
> > 
> > Cheers,
> > Jenny
> > 
> > At 11:43 AM 9/24/2007, James MacDonald wrote:
> >> Martin Morgan wrote:
> >>> Probably in Jim's use it makes sense to have parent=emptyenv(),
> >>> otherwise you can 'get' symbols that are defined in the global
> >>> environment rather than the environment you're looking in.
> >> Yup. My bad. I was thinking .GlobalEnv wasn't right, but I couldn't
> >> remember what parent=NULL used to do. Thanks for the heads-up.
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >>
> >> --
> >> James W. MacDonald, MS
> >> Biostatistician
> >> UMCCC cDNA and Affymetrix Core
> >> University of Michigan
> >> 1500 E Medical Center Drive
> >> 7410 CCGC
> >> Ann Arbor MI 48109
> >> 734-647-5623
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives: 
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> > 
> > Jenny Drnevich, Ph.D.
> > 
> > Functional Genomics Bioinformatics Specialist
> > W.M. Keck Center for Comparative and Functional Genomics
> > Roy J. Carver Biotechnology Center
> > University of Illinois, Urbana-Champaign
> > 
> > 330 ERML
> > 1201 W. Gregory Dr.
> > Urbana, IL 61801
> > USA
> > 
> > ph: 217-244-7355
> > fax: 217-265-5066
> > e-mail: drnevich at uiuc.edu
> > 
> > _______________________________________________
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> >
> 
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