[BioC] GO over representation analysis

[James W. MacDonald]

michael watson (IAH-C) wrote:
> 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?  

My understanding is that this is part of the plan. Marc would know 
better, and will also have a better idea of the timeline for such tools 
to appear.


> 
> -----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