Acceptable levels of quality-related variables were determined based on empirical observation of samples with relationship and DNA quality issues.
The choice of 30 samples was based on empirical discovery of the minimum number of one second samples needed to provide a stable average score, as follows.
We found that the difference in allele frequency at the PHYC locus (Fig. 5B) exceeded the simple effect of drift and sampling based on empirical (P<0.02) or model-based distribution of differentiation (p<0.001).
Provided that the current sequencing cost for Hiseq 2000 (based on the list price from the manufacturer) is approximately $40 per gigabase, the sequence yield per run is 600 Gb [ 49], and the sequencing volume needed to reveal insect richness from bulk samples (based on empirical data of this paper), we calculate the average cost for discovering a single insect species is less than $20.
For SAM the moderated t-statistic (d score) does not have an associated distribution theory so estimates of reliability are based on empirical FDRs calculated from balanced permutations of samples [20].
In fact, the between-template and between-subject variability are acknowledged based on empirical estimates, the latter being additionally gauged by individual sample size (Eickhoff et al. 2009).
The system is based on arbitrary cut-points such as sample size above 50 and more than 80% follow-up, which are not based on empirical evidence.
The term, they object, suggests that the minority position is actually based on empirical data.
