I have experimental values for a large set of genes that are NOT coming from sequencing. They are image analysis derived GFP intensities. From these values, some of those genes are interesting and some are not so I could if needed define a set of "interesting" genes. But I would prefer to take the actual experimental values into account.
I would like to analyse my interesting genes and understand what pathways and bioprocesses are triggered (compared to the rest of my genes).
I have seen many get set enrichment analyses but they all seem to work on p-values (or other stats) or log fold changes (like GAGE). May I ask some expert views on what tool I should use please? Could I use CAGE for instance and replace the log fold changes as input by the intensities?