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FTO-SNP rs1121980 rendered the lowest nominal p-value of 1.13×10−7; this SNP was the only SNP that survived correction for multiple testing (corrected p = 0.0494; Table 1).
The multiple testing corrected P-values (Benjamini correction) are reported.
We identified four regions which showed an excess of deletions in controls, but these regions did not remain significant after correction for multiple testing (corrected P > 0.4).
The strongest finding of our study was the association of a nonsynonymous DAOA variant, rs2391191 (Arg30Lys), with visuospatial ability, which remains significant after a conservative Bonferroni correction for multiple testing (corrected p =.005).
In order to detect Gene Ontology (GO) terms that are overrepresented in a gene subsample of interest against all T. castaneum genes as background, we applied Fisher's Exact Test with a multiple testing corrected p-value cutoff of 0.05 and generated a TermLogo similar to [ 12].
We therefore performed an FDR correction using "p.adjust" and provided the list of multiple testing corrected p-values in the additional files (Additional file 1).
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Both the non-multiple testing corrected p-values and Bonferroni adjusted p-values are ranked and displayed.
For gene extraction, a multiple-testing corrected t-test (the so-called q-value) is employed.
(4) During the past decade, several algorithms have been developed for both the normalization and summarization of raw data (robust multichip algorithm, MAS5, PLIER, etc) and to obtain differentially expressed gene lists (fold-change thresholds, multiple-testing corrected t-test, rank product, significance analysis of microarrays, linear models for microarray data, etc).
From a total of 22810 genes represented on the array, genes differentially expressed between experimental samples and controls were detected using two-sample t-tests with a multiple-testing corrected p-value of 0.05 used as the cutoff.
Tukey's test was used to calculate multiple-testing corrected P-values for all pairwise comparisons of plant families.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com