Exact(15)
We chose a FDR <0.033 to define significance as this translated to the false discovery of 1 physical cluster.
To minimize false discovery of DMEs, the detection threshold value was chosen to ensure that the number of DMEs identified in unenriched DNA was less than 5% of that identified in an His-MBD enriched sample from the same source (Supporting Information S1).
To limit false discovery of QTL, we performed permutation tests to establish an α = 0.01 comparisonwise threshold (CWT) for each test position (Doerge and Churchill 1996).
In addition to false negatives in single-cell analysis due to ADO, false discovery of mutations is also a major concern.
Recombination can lead to false discovery of positive selection using the dN/dS ratio, leading to erroneous interpretation of the impact of selection across genomes (Anisimova et al. 2003; Arenas and Posada 2010a).
Each method is associated with artefacts introduced due to allelic drop out (ADO), preferential amplification of certain genomic sites and false discovery of mutations due to amplification or sequencing errors (7).
Similar(45)
Thus, FDR of 1% is a reasonable estimate of the "true" false discovery rate of the top 68 DPGs.
By choosing a p-value of 0.01 a false discovery rate of about 5% was calculated.
Using a false discovery rate of 0.05, a total of 1,497 differentially expressed genes were identified.
To control false positive discovery rate we apply Benjamini-Hochberg correction: ∗represent Benjamini-Hochberg critical value with a false discovery rate of 0.2; and the rest of points - critical value for a false discovery rate of 0.1.
P values ≤ 0.01 had a false discovery rate of 45.3% and P values of ≤ 0.001 had a false discovery rate of 26.5%.
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