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

[J.delasHeras at ed.ac.uk]

Dear Wolfgang,

thanks for your reply. Yes, the annotation support part in some of the  
vignettes I looked at was throwing me out a bit.

Jose (no, still haven't changed my name ;-)

Quoting Wolfgang Huber <whuber at embl.de>:

> 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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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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