We have a big patient cohort and are wondering on the best ways to integrate the data. So far we have been using WGCNA on the microarray data with moderate success, but the question is how to we approach this when multiple genomic platforms must all be integrated? So we are interested in clustering the data using the platforms together with respect to clinical data (consensus clustering, iclusterplus), then also prediction of prognosis, and also network construction/ module generation with correlations to clinical data (WGCNA, ARACNE). Does anyone have any advice here? Any neat packages I am missing?