These p-values were then adjusted for multiple comparisons by using the false discovery rate approach (FDR) [26].
The correction for multiple comparisons was performed by using the false discovery rate option in GOstat.
Correction for multiple comparisons was accomplished by using the false discovery rate method using an alpha of 0.05 and a subroutine within MethLAB [ 28].
Multiple testing corrections were performed, and the P values were adjusted by using the false discovery rate (FDR) method, with the family-wise error rate of P <0.05.
The significance level was determined by using the false discovery rate (FDR) test at a level of 0.05 [ 33], which allows type-I error detection.
Enrichment-adjusted JEPEG gene-level P values were subsequently adjusted for multiple testing by using the false discovery rate (FDR) procedure.
The p-values for all statistical tests were estimated by the permutation method using residual shuffling, followed by adjustment for multiple comparisons by using the false discovery rate (FDR) approach [ 37].
In a second step, statistical significance is estimated by using the false discovery rate (FDR) methodology [ 20] which results in the assignment of a q-value for each gene.
Significantly, DE contigs were determined by using the false discovery rate (FDR) of Storey and Tibshirani (2003) to adjust gene-specific P values for multiple tests, taking a significance threshold of 5% FDR.
