The mapping performed on the 78730 mutant used a subset of the available markers on both arrays: 30,000 SFP markers were used, although, permutation testing suggests that 100,000 SFPs could be used with a false discovery rate of 0.05.
The False Discovery Rate tool 'Significance Analysis of Microarrays' (SAM v3.0; [ 8] was used with a false discovery rate of 10%.
For calling gains and losses in array CGH data, the Analysis of Copy Errors (ACE) algorithm in CGH-Explorer [ 20] was used with an False Discovery Rate (FDR) <0.01.
Utilizing the B. bronchiseptica long-oligonucleotide microarray, ratio data collected from microarray analysis involving the direct comparison between B. bronchiseptica RB50 and RB54 revealed 1,668 Bvg-regulated genes (identified using SAM with a false discovery rate of <0.1%).
Differential expression analysis for the tumor specimens was performed using ANOVA with a False-Discovery Rate (FDR) <0.05, 2-fold change defining differential expression.
Significance analysis of RNA-seq data was used to identify those genes significantly up- or down-regulated by treatments using unlogged data, with a false discovery rate (FDR) less than 0.05.
A moderated t test [ 40] was performed in parallel, with the use of a false discovery rate [ 45] correction for multiple testing.
An unnamed "brave individual" also managed to pass letters to the activists from the outside world, while Ball used a matchbox with a false bottom to smuggle his film footage out to the global press.
We used univariate tests with a false discovery rate (FDR) correction that adjusts the significance level for multiple tests.
Figure legend 3 has been altered to include these details: "Sites were determined by identifying the DNase1 sites common to K562 and HeLa cells, as defined by the ENCODE project, that contained the 19 bp CTCF consensus binding motif (MA0139.1) by using FIMO analysis with a false discovery rate of 0.01.
