![]() # P P.permuted P.adjusted.perm P.adjusted. While cleavage with cpCasp2 is possible before all 20 proteinogenic amino acids, cleavage before valine, leucine, isoleucine, aspartate and glutamate suffers from slow, and before proline extremely slow, turnover. P.adjusted.BH = round(p.adjust(p, method = "BH"), 4) The circularly permuted caspase-2 (cpCasp2) with its specific cleavage site, efficiently generates the untagged protein. This example also shows the discrepancy between the permutation-adjusted P values and Benjamini-Hochberg-adjusted P values. pseudo-random numbers through algorithms that mimic randomness, which we use to shuffle or permute the errors. This happens also with a higher number of permutations, e.g. How many permuted data sets should I use. Benjamini-Hochberg-adjusted P"Īn example where permutation-adjusted P values increase, but (unadjusted) permuted P values decrease: For a planned trial with 2n patients, specify an amount of imbalance that would be unacceptable. Sum(x <= x) / length(x) # x is the original P valueĬalculate P values adjusted for multiple comparisons using permutation testing:īased on this link. Matrix(, nrow = n.perm, ncol = length(p)) P, # Original P values included as one of the permutations. Wilcox.test(x ~ Ionosphere $Class)$p.value # Column 33: binary dependent variable ('Class': bad/good).Ĭalculate original and permuted P values: # Calculate original P values: # Columns 1-32: continuous independent variables. Ionosphere <- Ionosphere # Remove factor variables. Here is the code: Prepare example data: library(mlbench)
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