[BioC] PANTHER in R.... Gene lists in sigPathway?

[Ovokeraye Achinike-Oduaran]

Hi Felipe,

Thanks. The thing is that I have genes from both GWAS and DE analysis from Limma in one list. So they don't all have logFC values, hence my question about gene lists and not necessarily gene sets. I ran my list through the PANTHER web interface and got some results but I just wanted to know if it had an R implementation. 

DAVIDQuery() might work if it gives the same options as is web interface of choosing the PANTHER pathway option but I didn't find the instruction manual very straightforward.

Thanks again.

-Avoks




On 22 May 2012, at 6:17 AM, Felipe Riveroll Aguirre <friveroll at gmail.com> wrote:

> Sorry I forget to write, this text for the first paragraph
> 
> There is no bioconductor project, for pantherdb, but you can get a tab
> separated file with entrezID and logFC data from limma for example,
> and upload the generated file to the pantherdb website Tools>GENE
> EXPRESSION DATA ANALYSIS>Analyze a list of genes with expression
> values
> 
> 
> Felipe Antonio Riveroll Aguirre
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> 
> 
> 2012/5/21 Felipe Riveroll Aguirre <friveroll at gmail.com>:
>> For the first question.
>> 
>> There is no bioconductor project, for pantherdb, but you can get a tab
>> separated file with entrezID and logFC data from limma for example