[BioC] GOstats - zebrafish

[Neel Aluru]

Hello BioC users,

My question is pretty vague, so please bear with me. I want to do Gene set enrichment analysis (GSEA) on zebrafish agilent array data. I read the user guide and vignettes but still it is not quite clear to me how to proceed with it. What I have with regard to annotation of my probes is gene name, gene bank accession numbers and probe sequences. Using this information, is it possible to get GO annotations for my probes with any of the packages available. Zebrafish annotation package (org.Dr.eg.db) has objects such as org.Dr.egGO2EG, org.Dr.egGO etc. Is it possible to map with them and then you those data in GSEA? Most of the examples are on affymetrix data and I cannot seem to find literature where it is used on agilent arrays.

Any suggestions or comments will be appreciated.

Thank you,

Neel

Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607