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Contrasts with p < 0.05 were considered significant (with no multiple correction adjustment).
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For differential gene expression, three biological replicates per sample were then subject to statistical tests, using the samWrapper package (DEGseq version 2.6; http://bioconductor.org/packages/release/bioc/html/DEGseq.html) in R (www. r -project.org) followed by multiple correction (FDR ≤ 0.001).
These 53 targets were significant (p-value < 0.05) against all three background sets and significant following Benjamini-Hochberg multestingesting correction (BH adjusted p-value < 0.05) against at least two of the three background sets.
After multiple correction, four BP terms were significant at p < 0.05.
A complete methodology was implemented for developing the proposed method, including an experimental design, data preprocessing by using multiple scatter correction (MSC) and outlier detection based on high values of leverage, and X and Y residuals.
This association was still significant after multiple testing correction (PFDR = 0.026).
Q-values are derived from P-values by applying a Multiple Testing Correction (MTC) procedure.
The hypergeometric test was used with Benjamini and Hochberg multiple testing correction (FDR = 0.05).
In the set with multiple testing correction, GO enrichment analysis was performed at a significance level of 0.05.
Bonferroni multiple testing correction (MTC, αBonf < 0.05) was applied to identify only those genes with the most robust changes.
Both polymorphisms were significantly associated with joint damage after multiple test correction (PFDR = 0.014 and PFDR = 0.040 for rs4845618 and rs4845374, respectively).
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