If you use this code, please cite : Y. Qi, HK. Dhiman, et al, Z. Bar-Joseph, J. Klein-Seetharaman,(2009) "Systematic prediction of human membrane receptor interactions" PROTEOMICS 2009, 9, 5243-5255 --------------------------------------------- I assume that you have the "g77" command in your command list. (all unix machines have this.) If not, for windows, you can install the software: "MinGW". Remember to make the g77 in your windows command list after installations. --------------------------------------------- It is very easy to run this code: 1. Just put your parameter in a parameter file for example: testpara.file totally 10 parameters (all related files' names should be also in the input parameter file.) 2. Then run the perl wrapper perl change_RF_codeRunParaF.pl testpara.file --------------------------------------------- I assume that your input feature files have been pre-processed ==> which means they contain all real features and the features have no missing values. --------------------------------------------- In the subdirectory, there exsit the example files configurying in the "testpara.file" --------------------------------------------- perl wrapper "process_RFtestOut.pl" is an extra script. Since the RF output contains the voting from all trees about postive leaves or negative leaves.. Thus one summary score could be just the ==> positive vote score - negative vote score This wrapper would convert the direct output RF file into the summary score file as described.