# Input file for bgx samples 1 conditions 1 probes 16220 genes 1011 # The files containing the data and the structure of the experiment. These # filenames must not contain white space. SampleSets data/SampleSetsSS.txt ProbeSets data/ProbeSets.txt PM data/PM.txt MM data/MM.txt seed 192492 sweeps 32768 burn-in 8192 # Which (approximate) quantiles of the thetas do you want? These are # calculated using Luke Tierney's method for sequential quantile estimation Quantiles 3 0.025 0.5 0.975 # What output do you want? # minimal Just output the mean and approximate quantiles of theta for # each gene/condition pair. # trace Also output a trace of theta, subsampled at equally spaced # intervals so that you get around 1024 values for each # gene/condition pair. # diagnostic Also output traces for the low-dimensional parameters and # posterior means and approximate medians for the # high-dimensional parameters. # mcse Calculate Monte-Carlo Standard Errors for each theta. This # option should only be used if you either (a) have a very # small dataset (genes x samples < 10000) or (b) you have # an enormous amount of memory AND you are running the program # on a 64 bit machine. If these conditions are not met the # program will fail without warning. Output trace # I recommend that you don't touch any of the options below this line # unless you REALLY know what you are doing. S_jmp 150 H_jmp 350 Mu_jmp 1.1 Tau_jmp 1.5 Lambda_jmp 0.04 Eta_jmp 0.1 Init_size 100