[BioC] GO over representation analysis

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Aug 29 15:15:30 CEST 2008


OK, so there is not chicken.db0 or cow.db0 package so that rules that
one out. 

My experience is that most people have a "star" schema of information
linking probes to genes to GO IDs, Pathways, Entrez etc etc.

It *should* be simple to make an annotation package out of this, but it
isn't.

And I hate to be hper-critical but the Vignette for AnnBuilder is
virtually inaccessible...

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: 29 August 2008 14:07
To: Sean Davis
Cc: michael watson (IAH-C); bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GO over representation analysis

There is one slight additional wrinkle. AnnotationDbi currently supports

fewer species than AnnBuilder. Building a package using AnnotationDbi is

(at least) a two step process, of which only one is required of the end 
user. The first step(s) are to build a database containing all relevant 
data for a given species that is then used to populate the chip-specific

package databases.

If you are interested in an annotation package that is not yet supported

by AnnotationDbi, then you will need to consult with Marc Carlson to get

the primary database built.

Best,

Jim



Sean Davis wrote:
> On Fri, Aug 29, 2008 at 8:33 AM, michael watson (IAH-C)
> <michael.watson at bbsrc.ac.uk> wrote:
>> Dear All
>>
>> I think one thing that is frustrating here is that there is not a
simple
>> guide here for people who want to create an annotation package for an
>> array that does not yet have one.
>>
>> Do we use AnnotationDbi?  Or AnnBuilder?  Or is there another way?
>>
>> What is the "best practice" for building an annotation package?
> 
> Hi, Mick.  The confusion arises because annotation packages have been
> migrated from the environment-based packages built by AnnBuilder to
> the newer SQLite-based packages of AnnotationDbi.  The answer depends
> on which version of R and, therefore, which version of Bioconductor
> you are using.  That said, the standard for the current and future
> releases (for the near-future, anyway) is to use SQLForge from
> AnnotationDbi.
> 
> Sean
> 
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc
>> Carlson
>> Sent: 25 August 2008 17:03
>> To: Heike Pospisil
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] GO over representation analysis
>>
>> You could just make an annotation package for the array in question
by
>> using the SQLForge code in the AnotationDbi package.
>> You can find instructions on how to do this here:
>>
>> http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html
>>
>> Let me know if you have any questions about SQLForge.
>>
>>
>>  Marc
>>
>>
>>
>> Heike Pospisil wrote:
>>> Hello Bioconductors,
>>>
>>> I am looking for a method to perfom over representation analysis
(Gene
>>> Ontology) within R. I have data from the Maize Oligonucleotide Array
>> (two
>>> channel) with the GO categories for all probes on this array. I have
>>> clustered the genes using Maanova and I am interested in GO over
>>> representation of the gene lists from these clusters.
>>>
>>> I know the GO tools from Bioconductor (e.g. GOstats), but I do not
>> know how to
>>> adapt the analysis to an 'unusual' array with no annotation data
>> package and
>>> now Entrez IDs. Any hints?
>>>
>>> Thanks in advance,
>>> Heike
>>>
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662



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