[BioC] bovine Annotation package(s)
Louisa A Rispoli/AS/EXP/UTIA
larispoli at mail.ag.utk.edu
Thu Jul 31 16:08:25 CEST 2008
Hi Nathan-
I would greatly appreciate it if you could send the package. A grad student
trying to finish her PhD and I are trying to understand annotation so we
can apply to the gene lists we finally figured out how to do our linear
model, ebayes and fdr on. We are really frustrated since most
packages/software only has info for human, mouse, or drosophila and we
think cows are kind of important. Any help would be appreciated since we
are new to this and want to be as accurate as feasible. Thanks
Louisa
"If we knew what we were doing, it wouldn't be called Research." - Albert
Einstein
Louisa Rispoli, Ph.D. Reproductive Physiology
Department of Animal Science
University of Tennessee, Knoxville
A105 Johnson Animal Research and Teaching Unit
1750 Alcoa Highway
Knoxville, TN 37920
phone:(865) 946-1874
fax:(865) 946-1010
email: lrispoli at utk.edu
"Nathan S. Haigh"
<N.Haigh at sheffiel
d.ac.uk> To
Louisa A Rispoli/AS/EXP/UTIA
07/30/2008 07:24 <larispoli at mail.ag.utk.edu>
PM cc
Marc Carlson <mcarlson at fhcrc.org>,
bioconductor at stat.math.ethz.ch
Subject
Re: [BioC] bovine Annotation
package(s)
Hi Louisa,
Just to clarify with a few things I've learnt in the last week or two
regarding the Bioconductor annotation packages/framework.
There are currently two types of annotation packages:
1) Those built by AnnBuilder
2) Those built by SQLForge
The former are the older style annotation packages which I believe are
being replaced by the latter. The latter are better as the annotations are
actually stored/distributed in a database format using SQLite and are
linked to online resources so are far more extensible than the old flat
file
format. However, the latter requires a certain amount of
configuration/setup by the bioconductor devs to create a *.db0 package (not
distributed with
BioC) for a given organism which are used to generate the "real" annotation
package which is distributed with BioC. As a result, if you need an
annotation package for an unsupported organism (I think there are currently
7), you need to ask the devs nicely to build the *.db0 package or you can
use AnnBuilder to build an old-style annotation package.
I have built such a file for the affymatrix bovine chip. However, there are
limitations (which I don't yet fully understand) to what packages you can
use to analyse the annotations - not sure it it's because those packages
expect the new style *.db annotation packages or not. I need to figure out
exactly what the issue are, but I can send you the package if you like?
Cheers,
Nathan
Quoting Louisa A Rispoli/AS/EXP/UTIA <larispoli at mail.ag.utk.edu>:
> Marc-
>
> I was wondering how it was going with building a bovine annotation
> database? I have been reading through the vignette for AnnBuilder and not
> sure that I have the skills for building the bovine.
>
>
> Is there something else that I need to be reading to assist? Thanks
>
> Louisa Rispoli
>
> "If we knew what we were doing, it wouldn't be called Research." - Albert
> Einstein
>
> Louisa Rispoli, Ph.D. Reproductive Physiology
> Department of Animal Science
> University of Tennessee, Knoxville
> A105 Johnson Animal Research and Teaching Unit
> 1750 Alcoa Highway
> Knoxville, TN 37920
> phone:(865) 946-1874
> fax:(865) 946-1010
> email: lrispoli at utk.edu
>
>
>
>
>
> Marc Carlson
> <mcarlson at fhcrc.o
> rg>
To
> Sent by: Sean Davis <sdavis2 at mail.nih.gov>
> bioconductor-boun
cc
> ces at stat.math.eth Nathan.Watson-Haigh at csiro.au,
> z.ch bioconductor at stat.math.ethz.ch
>
Subject
> Re: [BioC] bovine Annotation
> 07/16/2008 01:21 package(s)
> PM
>
>
>
>
>
>
>
>
>
> Hi Nathan,
>
> What Sean says is true. However, I have not yet made a bovine.db0
> database, so it is not yet possible to make .db annotation packages for
> bovines. However, if you would be willing to work with me a little bit,
> I would be willing to look into it. Lets take this off line and explore
> it a little bit. In the meantime part of the reason that AnnBuilder is
> still alive is because of odd corner cases like this one where someone
> needs support for an unusual organism. So you should be able to use
> AnnBuilder in the interim.
>
> Marc
>
>
>
>
> Sean Davis wrote:
> > On Tue, Jul 15, 2008 at 8:08 PM, <Nathan.Watson-Haigh at csiro.au> wrote:
> >
> >> I'd like to be able to conduct metadata analyses on things such as GO
> >> with data I have from an Affymetrix bovine chip. I've not done this on
> >> other arrays, so I'm not sure what is needed to do this.
> >>
> >> I saw that there were no bovine or bovine.db packages available, so I
> >> used AnnBuilder to create a bovine package from the GenBank IDs
provided
> >> by Affymetrix. My question/confusion is what's the *.db packages for,
do
> >> I need one for the bovine chip, and how would I make one?
> >>
> >
> > The *.db packages are the new standard for annotation packages. Have
> > a look at how to create one by looking at the AnnotationDbi package
> > and, specifically, the SQLForge vignette.
> >
> > Sean
> >
> > _______________________________________________
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> >
> >
>
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