I came across your paper, "Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostrate Cancer". I am having trouble finding an appropriate algorithm to find dysregulated pathways from large clinical expression arrays and was impressed with the method you implemented. I was wondering if you happened to have the source code you used to implement IMAP and if it was possible for me to take a look at it. If so, that would be of enormous assistance to me.
Unfortunately there is no code floating around to perform the analyses you want to do. I did the calculations for the paper you cited but I did them three years ago and the computations were done mostly interactively in an R terminal.