[BioC] GO over representation analysis

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Aug 29 16:59:31 CEST 2008


I am sure Marc would be very accomodating :)

What would be excellent, however, is if I could create a db0 package
myself.
I have all the data - all the links from ensembl, entrez, GO, KEGG,
Unigene etc. 

Is it planned to provide tools to create db0 packages?  

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: 29 August 2008 15:50
To: michael watson (IAH-C)
Cc: Sean Davis; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GO over representation analysis

michael watson (IAH-C) wrote:
> OK, so there is not chicken.db0 or cow.db0 package so that rules that
> one out. 

Really? Does this mean you contacted Marc Carlson about creating 
packages for these species and he told you it was out of the question? I

would find that rather surprising. In the past (and a quick search of 
the BioC listserv bears this out), he has been rather accommodating.

> 
> 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...

Yes, well it is a bit much to ask that the vignette for a soon to be 
deprecated package be updated, no?

> 
> -----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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> 

-- 
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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