I have a list of probes (up regulated genes) and I have a gene set (consists of several column of probes which have been already ranked based on their expression) 

Now, I want to perform  Kolmogorov-smirnov test or pre ranked GSEA. can any body help with how to do it ? you can find an example data in the following links

Hi Nemo,

You can use the topGO package, the vignette shows example on how to do it :)

use fgsea bioconductor package.