Exact p-Values for Network Interference

Computing exact P-values for DNA motifs

MOTIVATION Many heuristic algorithms have been designed to approximate P-values of DNA motifs described by position weight matrices, for evaluating their statistical significance. They often significantly deviate from the true P-value by orders of magnitude. Exact P-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the problem is unknown. RESULTS...

Computing exact p - values for DNA motifs ( Part I )

Motivation: Many heuristic algorithms have been designed to approximate p-values of DNA motifs described by position weight matrices, for evaluating their statistical significance. They often significantly deviate from the true p-value by orders of magnitude. Exact p-value computation is needed for ranking the motifs. Furthermore, surprisingly, the complexity of the

Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn.

Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permuting the sample or gene labels. Yet permutation p-values published in the genomic literature are often computed incorrectly, understated by about 1/m, where m is the number of permutations. The same is often true in the ...

Exact P - values in Incomplete Multi - way Tables ∗

I develop a new Markov chain algorithm for sampling from sets of multi-way contingency tables defined by an arbitrary set of fixed marginals and by lower and upper bounds constraints on cell counts. My procedure is called the Bounds Sampling Algorithm (BSA) and it relies on the existence of a method to calculate lower and upper bounds for cell entries. BSA accommodates any pattern of structural...

Computing highly accurate or exact P-values using importance sampling