The resampling is taking too long, any suggestions?
This problem affects the correlation score analysis in particular, which is very computationally intensive. There are few ways to speed things up. One is to uncheck the “Always use full resampling” checkbox in the analysis setup wizard. This enables approximations which, while potentially yielding less accurate p-values, greatly increase processing speed. The results you get with this box unchecked will be reasonably similar to what you would get with full resampling. Another tip is to not look at very large values for the “maximum class size” value. We usually use a value on the order of 200. Finally, you can reduce the number of iterations. You might try temporarily setting this to 10000 while you experiment with the other settings, and then, once you find a setting you like, you can crank up the iterations for the “final” run (for example to 200000, which still should not take very long for the gene-score based resampling).
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