Repo for BIOS 784 Computational Biology Project (Bladder Cancer)
Looking at GSE1827 (all subjects have cancer)
Intro: -Background -Show the clustering diagram of the 80 tumors into superficial/invasive clusters and describe -Re-create this cluster diagram
Goal #0 (Recreate from Paper) -Do clustering on the whole thing (exploratory analysis)
Goal #1 (Gene Set selections) -Examine difference between invasive and superficial tumors using our methods from class (lmfit) -> find set of genes predictive of this outcome (not controlling for anything) -Use multiple p-value cutoffs (.001, .0001) and compare the results -Use different sample sizes -Compare to random and row variance selections
Goal #2 (Predictions) -Using gene sets from #1, use different methods and cross validation sizes to predict
Steps forward from Nov 8: -Each work with/play around with goals 1 and 2 -At next meet work on comparing different gene sets we get for #1 - Also compare different methods