Dear users & developers,

i'm sure that there were discussions about the pros and cons of switching to
.db packages before the actual decision
was made. Personally i don't really understand why it is not possible to
have the old style packages. If anyone
can point me out the pro's of having the .db packages, or just forward me to
the relevant arguments (assuming they
are public), i would be really grateful.

For me, environment-based packages are much better, because they're faster,
and i have enough RAM to load
everything at the same time. Here is a little demonstration:

> library(org.Hs.eg.db)
>
> egGO <- new.env(hash=TRUE)
>
> all <- mget( ls(org.Hs.egGO), org.Hs.egGO )
>
> for (i in seq(all)) {assign(names(all)[i], all[[i]], envir=egGO) }
>
> sam <- sample(ls(org.Hs.egGO), 5000)
> system.time( tmp <- mget(sam, org.Hs.egGO) )
   user  system elapsed
  0.808   0.001   0.811
> system.time( tmp <- mget(sam, egGO) )
   user  system elapsed
  0.022   0.000   0.023
>

You could argue that the slower query is still under one second, and it does
not matter, but it actually does matter if you have lots
of queries.  For some of my scripts the difference is something like 1 day
agains 10 minutes. E.g. GO enrichment calculation
can be speeded up about 100 times if one uses the environment based packages
and tailors the original hyperGTest for GO
a bit.

It is interesting to see that in R, the direction was "storing everything in
memory" instead of keeping the data on the disk,
as many other statistical software packages do; here, however, the direction
is the opposite. You can also argue that these
data packages are getting bigger and bigger each year, but so do the size of
the RAM in the computers. For me it
is not obvious which curve is steeper.

Finally, it might happen that the .db packages are just as fast as the old
ones, only i'm not using them the right way.
If this is the case, then i apologize, please show me the right way.

Best Regards,
Gabor

On Wed, Apr 16, 2008 at 11:36 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Richard,
>
> In general you want to use the .db version of these packages as it is
> the newer format.
>
> The older format is really only provided for people who have lots of
> old-style package dependencies that they still need to work out.  In a
> couple of weeks, we should have a new version of these packages for you
> to explore.  But the older format will be deprecated which means we are
> not planning to make it again after the upcoming release...
>
>
>    Marc
>
>
>
>
> Richard Friedman wrote:
> > Dear bioconductor list,
> >
> >       The mouse4302.db annotation package is listed as Version 2.02 of
> the
> > annotation
> > for mouse 4302 and was packaged Mon Oct 22 10:15:57.
> >
> >       The mouse4302 annotation package is listed as Version 2.01 and was
> > packaged
> >   Thu Oct 11 11:31:47 2007.
> >
> >       Should I there use mouse4302.db as the more recent and
> authoritative
> > of the 2 packages?
> > Or is it simply one with different contents?
> >
> >       I realize that the answer to this question may seem pretty obvious
> > but I am wondering
> > why mouse4302.db has a different name and not simply the same name
> > and a different version number.
> > So I thought I would ask to make sure.
> >
> > Thanks and best wishes,
> > Rich
> > -----------------------------------------------------------
> > Richard A. Friedman, PhD
> > Associate Research Scientist,
> > Biomedical Informatics Shared Resource
> > Herbert Irving Comprehensive Cancer Center (HICCC)
> > Lecturer,
> > Department of Biomedical Informatics (DBMI)
> > Educational Coordinator,
> > Center for Computational Biology and Bioinformatics (C2B2)/
> > National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> > Box 95, Room 130BB or P&S 1-420C
> > Columbia University Medical Center
> > 630 W. 168th St.
> > New York, NY 10032
> > (212)305-6901 (5-6901) (voice)
> > friedman@cancercenter.columbia.edu
> > http://cancercenter.columbia.edu/~friedman/<http://cancercenter.columbia.edu/%7Efriedman/>
> >
> > In Memoriam,
> > Arthur C. Clarke
> >
> > _______________________________________________
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> >
> >
>
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