[BioC] Suggestion - gene set enrichment of genes against BP and Disease gene sets

[Atul Kakrana]

Hi Everybody,

I need your suggestion for the package to use so as to perform gene set 
enrichment analysis. I know the analysis directly relates to GSEAbase 
package but I not sure its the right one for the analysis I have in my 
mind. I need to make:
1. Heatmap of gene set enrichment of specifically enriched genes against 
various biological process and diseases categories/gene sets
2. Heatmap of gene set enrichment of specifically enriched genes against 
tissue specific gene sets

I have microarray data analyzed for 10 timepoints using 'affy' and 
'limma'. The results have 'probeId's and 'Gene Symbols' as identifier. 
My question is how do I approach and which
package should I use?

Thanks

AK