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In order to establish accurate empiric P-values we used a permutation based, topology-corrected method.
The pfp is calculated using a permutation based procedure (100,000 permutations were conducted).
We identified 740 probesets (640 genes) and 331 probesets (282 genes) using a permutation based FDR of 8.2%, and BH FDR of 5% respectively, as being differentially expressed between the two strains of mice.
Therefore, we chose to use a permutation-based method for computing the p-value for Kendall's tau.
We use a permutation-based approach that controls the family-wise error rate (probability of rejecting one or more true null hypotheses of no association).
As well as limiting the number of tests performed via specific hypotheses, we propose to use a permutation-based framework to control for multiple testing.
Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL.
Cluster significance was determined by a permutation based test, used to quantify the expected number of genes that would be assigned to each profile if the data were generated at random.
To determine significance level for a given cluster, a permutation based test was used to quantify the expected number of genes that would be assigned to each profile if the data were generated at random.
For hypothesis testing a permutation based Fs test was used [ 37] and the resulting P-values were corrected for false discoveries according to Storey and Tibshirani [ 38].
We evaluated the efficacy of the detection of Alternative Splicing Events (ASEs), using a linear model based algorithm (MiDAS) and a permutation based algorithm (RP).
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