[BioC] How to compare GO results

[Johannes Hanson]

Dear Alex and other list members,

The suggested script works nicely. However I get another problem when  
I using two specific lists of genes. The lists compare fine with all  
other lists but not with each other. I get the error only when I use  
onto='CC' or 'BP', but not 'MF'. Suggestions are most welcome.


My code:
 >library(goProfiles)
 >library(org.At.tair.db)
 >L2Plus26=compareGeneLists(MyList2,MyList6, level=2,  
orgPackage='org.At.tair.db', onto='CC')
Error in ancestors[[i]] : subscript out of bounds

 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-22 r48594)
i386-apple-darwin8.11.1

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] org.At.tair.db_2.3.4 goProfiles_1.7.0     GO.db_2.3.0           
RSQLite_0.7-2        DBI_0.2-4            AnnotationDbi_1.7.11  
Biobase_2.5.6

loaded via a namespace (and not attached):
[1] tools_2.10.0


On 19 Aug 2009, at 20:32, Alex Sanchez wrote:

> Hello
>
> goProfiles works with 'organism' anotation packages ('org.XXX.XXX.db')
> There is an Arabidopsis annotation package 'org.At.tair.db' in the  
> next version of BioC althoug I'm not sure if this is the one you need.
> You will find it in the Bioc-development site.
> http://www.bioconductor.org/packages/2.5/data/annotation/html/org.At.tair.db.html
>
> Once you have installed it the use with goProfiles should be  
> straightforward.
>
> For instance
>
> library(goProfiles)
> library(org.At.tair.db)
> tab1 <- toTable(org.At.tairENTREZID)
> genes <- sample(tab1[,1],100)
> ara.MF.Profiles <-basicProfile(genelist=genes, onto='MF', level=2,  
> orgPackage="org.At.tair.db",  empty.cats=FALSE)
> print(ara.MF.Profiles)
>
> will yield a basic profile at level 2 of the MF ontology for a  
> random sample of 100 Arabidopsis genes
>
> I have tried it with R-2.10.0 but it should work with R-2.9.z
>
> Alex
>
> -----------------------------------------------------------------------------------------------------
>
> Dr. Alex  Sánchez.
> Associate professor. Statistics Department. University of Barcelona.
> Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain
> asanchez_at_ub.edu
> Statistics and Bioinformatics Unit
> Institut de Recerca. Hospital Universitari Vall 'Hebron
> Passeig Vall d'Hebron 112-119. 08034 Barcelona
> asanchez_at_ir.vhebron.net
> ----------------------------------------------------------------------------------------------------
>
>
>
>
>
>
> ----- Original Message ----- From: "Johannes Hanson"  
> <s.j.hanson at uu.nl>
> To: "Alex Sanchez" <asanchez at ub.edu>
> Sent: Wednesday, August 19, 2009 11:25 AM
> Subject: Re: [BioC] How to compare GO results
>
>
> Thanks, THis software is answering most of the questions I have -
> excellent.
>
> However I am working with Arabidopsis data (Affymetrix ATH1 slides).
> As far as I understand the annotations files are not availible for
> arabidopsis. Is that something that can be solved no or in the future
> releases.
>
> Johannes
>
> On 15 Sep 2009, at 10:03, Alex Sanchez wrote:
>
>> Hi Johannes
>>
>> There are several packages in BioC that you can use to do GO   
>> analysis or to mine GO analysis results.
>> You can find most, if not all, of them in the Bioconductor GO task   
>> view. (Curiously topGO is not there).
>>
>> http://www.bioconductor.org/packages/release/GO.html
>>
>> I am the maintainer of the 'goProfiles' package which is, in   
>> principle, developed to answer the type of question you pose.
>> If you have any questions about its use I'll be pleased to try to   
>> help you at answering them.
>>
>> best
>>
>> Alex Sánchez
>>
>> ...............................................................................................................
>> Dr. Alex  Sánchez.
>> Associate Professor. Statistics Department. University of Barcelona.
>> Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain
>> asanchez_at_ub.edu
>> Statistics and Bioinformatics Unit
>> Institut de Recerca. Hospital Universitari Vall 'Hebron
>> Passeig Vall d'Hebron 112-119. 08034 Barcelona
>> asanchez_at_ir.vhebron.net
>> ...............................................................................................................
>>
>>
>>
>>
>>
>>
>>> Message: 17
>>> Date: Wed, 12 Aug 2009 09:10:56 +0200
>>> From: Johannes Hanson <s.j.hanson at uu.nl>
>>> Subject: [BioC] How to compare GO results
>>> To: bioconductor at stat.math.ethz.ch
>>> Message-ID: <02C00589-9261-449C-B8A4-D7C8C4986E72 at uu.nl>
>>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>>
>>> Dear all,
>>>
>>> This might not be a specific BioConductor question. However,
>>> BioConductor is my major tool and therefore I ask the question here.
>>> If not appropriate please ignore.
>>>
>>> I am analyzing array data from a set of mutants all showing the same
>>> phenotype. The idea was of course to find genes similarly  
>>> expressed  in
>>> all mutants to get closer to the regulatory mechanism of the   
>>> phenotype.
>>> Surprisingly there was nearly no overlap among the differentially
>>> expressed genes. The suggestion was raised that the genes might   
>>> encode
>>> similar functions. I therefore conducted GO analysis (using topGO  
>>> and
>>> other packages). Still very little obvious overlap but how to   
>>> quantify
>>> it? How to determine the degree of similarity between different GO
>>> results?
>>>
>>> All suggestions are welcome.
>>>
>>> Johannes Hanson
>>> Molecular Plant Physiology, Utrecht University
>>>
>>>
>>
>
>