[BioC] GSEA, topGO, GOstats...? what's a good way to look at GO over-representation?

[axel.klenk at actelion.com]

Do we have something like the fortunes package for Bioconductor? I'd
nominate
the last paragraph from Wolfgang's message because I like it so much... :-)

> And if you do not care so much about automation, reproducibility and
> flexibility of your workflow, then using websites like mentioned by
> Michael to copy-paste your gene lists into might be the way to go.

Seriously, a very nice summary of why you want to use BioC...

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland



                                                                           
             Wolfgang Huber                                                
             <whuber at embl.de>                                              
             Sent by:                                                   To 
             bioconductor-boun         J.delasHeras at ed.ac.uk               
             ces at stat.math.eth                                          cc 
             z.ch                      bioconductor                        
                                       <bioconductor at stat.math.ethz.ch>    
                                                                   Subject 
             02/08/2010 05:55          Re: [BioC] GSEA, topGO, GOstats...? 
             PM                        what's a good way to look at GO     
                                       over-representation?                
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Dear Javier

Chapter 13 of the 'Bioconductor Case Studies' book is a good start, as
is
http://www.bioconductor.org/workshops/2009/SeattleApr09/gsea/GSEA_Lecture.pdf

and the vignette of the GSEABase package.

Let yourself not be confused by the fact that in some functions (eg
GOstats), there is support to make it easier to work with the
Bioconductor annotation packages (which are provided, among others, for
Affymetrix genechips). The concept of gene set enrichment analysis
itself is independent of where you get the gene sets from, and the
software above works with general gene lists.

And if you do not care so much about automation, reproducibility and
flexibility of your workflow, then using websites like mentioned by
Michael to copy-paste your gene lists into might be the way to go.

             Best wishes
             Wolfgang


J.delasHeras at ed.ac.uk scripsit 02/08/2010 05:29 PM:
>
> Dear list,
>
> I have a few gene lists derived from a human Illumina expression array.
> I just have Illumina IDs, I have gene names, and I have entrez gene IDs
> I obtained for them.
>
> I would like to analyse the list to look for over-representation of some
> category, probably using gene ontologies.
> I see there are several packages that seem to address this, although
> when I look at the examples I get the feeling they were designed with
> Affy arrays in mind and depend on an Affy array design...
>
> I am sure I am not the only one wanting to do this type of work on
> non-Affy arrays... I would appreciate a nudge towards the right package,
> or a way to "persuade" it to work with non-Affy array data, after all I
> imagine that all the array design is used for is the definition of teh
> genelists/universe and retrieval of the relevant GO ids.
>
> Thank you for any helpful comments.
>
> Jose
>


--

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact

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