Due to the overall high stringency of the experiment-wise significance threshold (the P exp ≤ 0.05 corresponded to a P marker ≤ 0.0001 marker-wise), small-effect QTL regions were also reported for those markers/chromosome regions with highly significant (P ≤ 0.01) marker-wise associations to the adjusted phenotypic means of one or more macro-environmental area.
Outcomes of experiments depend not only on experimental design but also on the stringency of conditions of the experiments: for example, too stringent conditions can lead to false negative interactions, as opposed to false positive results obtained from experiments that were not stringent enough.
As discussed previously, the appropriate level of QC stringency depends on the specific goals of the experiment and methods of analysis (Landt et al. 2012).
It is however difficult to say how large a cluster should be to be worthy of investigation since at the higher stringency of experiment #1 clusters we know to be of interest can be relatively small.
The choice of thresholds at intermediate levels will be dictated by the nature of the experiment and the required stringency that can be deduced from the ROC table.
For MAQ and BWA, which both report a quality score, we tested whether changing the stringency of the quality score cutoff in simulation experiments had any effect on the biases described here.
However, several pre-miRNAs were not detected due to the stringency of the filters but discovered with our direct cloning experiments, including bmo-miR-278, bmo-miR-306, bmo-miR-768, bmo-miR-1921 bmo-miR-1922 bmo-miR-1922 bmo-miR-1922R-1922. bmo-miR-1922 bmo-miR-1922 bmo-miR-1922
Differences in protocols, platforms, and number of replicate measurements can lead to significant differences in the stringency of the criteria used for detecting differential expression across experiments.
Built-in controls, both sample independent (including staining controls, extension controls, target removal controls and hybridization controls) and sample dependent (including stringency controls, nonspecific binding controls and nonpolymorphic controls), were inspected to assess the quality of the experiment.
While the stringency of the pluripotency tests available for mouse, reaching to the birth of mice from tetraploid complementation experiments [18], [19], [20] seems convincing, pluripotency of human cells is far less easy to prove.
