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To perform a statistical test not biased by the redundancy of the probe sets (more probe sets for the same gene), the computation of p-value of functional enrichment was based on the Entrez Gene assignment.
The computation of p-value of cumulative hypergeometric distribution was performed using the AS R77 algorithm [ 42].
Finally, group-level statistics were computed with non-parametric randomisation tests (FSL 5.0.4, http://fsl.fmrib.ox.ac.uk/fsl/) and threshold-free cluster enhancement for null-hypothesis testing and the computation of p-value maps.
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Second, the computation of the p-value: The p-value is a valuable parameter for the biomedical researcher since it measures the level of significance of any detected correlation.
Athey et al. (2015) develop methods for the computation of p values for three specific null hypotheses.
We performed an extensive analysis of the computation of P-values for matrices.
We used C++ for fast computation of P-values because Python was prohibitively slow.
Since the computation of P-values based on permutations is expensive we used the P-values from the F-test as the weight function.
The clusters are not numbered in the exact order of significance due to the limits of numerical precision in the computation of p-values.
Permutation testing and median statistics were employed to allow exact computation of p-values with minimal assumptions and the minimisation of outlier effects (Brammer et al., 1997).
So far, no tools have been developed allowing the computation of p-values for simultaneous occurrences of different motifs which can overlap.
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