By averaging a set of replicate measurements, the signal-to-noise ratio, S/N, will be increased [16].
This validation test included a set of replicate RNA from the microarrays plus six independent biological replicates.
To correct the potential bias resulting from this complex survey design, Statistics Canada recommends a bootstrap procedure using a set of replicate weights that they supply.
Scatter plots of the log2 expression measures between a set of replicates processed with different methods and Pearson correlation coefficients were prepared using Excel 2003 (Microsoft, Redmond, WA).
Of the 1,418,400 expression values measured in this experiment, 4489 (0.32%) were excluded as single outliers, and 1586 (0.11%) were excluded as a set of two outlying values in a set of replicates.
For example, consider one set of replicate spots with an average intensity of 128 (2) in one channel and 16384 (2) in the other channel compared to a set of replicate spots with an average intensity of 1024 (2) in one channel and 2048 (2) in the other channel (Fig. 2).
Per each depth, a set of seven replicated 100-mL narrow-mouth Winkler bottles was fixed immediately to evaluate the initial oxygen content, and two sets were incubated under light and dark conditions for 24 hours.
In order to contrast the main hypothesis of the manuscript, i.e., the existence of a network of genes underlying these complex phenotypes, we performed a formal network analysis with the LPHN3, NCAM1, TTC12, ANKK1, DRD2, and CDH13 genes, a set of significantly replicated genes either associated and/or linked to ADHD, disruptive behaviors, and SUD (Table 1).
