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The Wilcoxon rank sum test was utilized followed by multiple hypothesis correction [ 32- 34], and we required the corrected q-value to be less than 0.01 for a gene to be called differentially expressed.
Multiple hypothesis correction was done with the statsmodel library using the Benjamin-Hochberg method.
The Sect. "The filtering methodology" briefly discusses the filtering method and the need for a multiple hypothesis correction.
We add to the procedure proposed in ref. [10] a multiple hypothesis correction that we believe is necessary to minimize false positive [11].
Using arrest dates instead, gives a 0.48 hazard ratio for case management and 0.64 for medical services bThis association is not considered significant as it does not pass a multiple hypothesis correction Fig. 2 Effect of case management (a) and access to medical services (b) on arrest probability.
P-values were adjusted using a Bonferroni multiple hypothesis correction, where appropriate.
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For these conditions, however, no genes were found to be significantly differentially expressed, even before multiple hypothesis corrections to the p-values.
We leveraged the biological process and interaction properties of these multi-disorder autism genes to overcome the across-the-board multiple hypothesis corrections that a purely data-driven approach requires.
POTION reduces false positives through several sophisticated sequence and group filters based on numeric, phylogenetic, quality and conservation criteria to remove spurious data and through multiple hypothesis corrections, and considerably reduces computation time thanks to a parallelized design.
All statistical calculations (hypergeometric and Fisher's tests, and multiple hypothesis corrections) were computed by the R statistics package [ 36], which was accessed using the RPy package [ 37], a Python interface to R. The KEGG maps are coloured using the Python Imaging Library [ 38], using the co-ordinates provided by KEGG.
Eight pathways were significantly enriched after multiple hypotheses correction (q <0.05 [ 24], Table 1).
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CEO of Professional Science Editing for Scientists @ prosciediting.com