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Preservation was calculated using permutations of the preservation statistics and is represented by a Z-summary value.
Pair-wise analyses using permutations of Mahalanobis distances produce the same pattern (Additional file 3: Table S1).
The significance of differences was assessed using permutations of pair-wise Procrustes distances among all possible pairs of taxa.
The same pattern is produced by pair-wise analyses using permutations of Mahalanobis distances (Additional file 3: Table S2).
A subsequent parallel analysis (using permutations of the raw data) revealed that a two-factor solution was optimal, which explained 54.12% of the variance (Table 3).
We have shown previously that the analytical q-value estimates are similar to those obtained using permutations of sample labels preserving the potential correlative structure between CpGs [ 31].
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Calculation was performed by estimating the sampling distribution using permutation of inputs (cf. permutation tests).
Significance is estimated using permutation of samples; however, the test statistic is standardized using gene scores calculated for all the genes in the study.
The Shapiro Wilk test does not reject normality for most probesets, and spot checks using permutation of the genotype factor gave similar P-values.
However, they used permutations of variables and distinguished between the first and the last variables.
To identify genes differently expressed in relation with brain aging or pathology, filtered data were analyzed with the SAM (Significance Analysis of Microarrays) method [44], which uses permutations of repeated measurements to protect against non-normal data distribution.
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