The p-value thresholds were related to marker number, with the single SNP and TreeScan thresholds being the most stringent and the HapBlock threshold, with the fewest markers (Table 2), being the least stringent (Figure 2).
In total, 2,530 up-regulated and 2,488 down-regulated genes were identified (Figure 2B) using a stringent threshold value to minimize the number of false positives (FDR below 0.25%).
However, confluent A549-NT cells appeared as cobblestone monolayer, characteristic of epithelial cell growth, consistent of closely associated cells with a typical polygonal, epithelial-like morphology indicating a stringent contact inhibition of cell growth (Figure 1B).
A stringent assembly pipeline was implemented and is summarized in Figure 1.
The volcano plot for each condition (Additional file 3: Figure S2) was analyzed by employing a stringent cut-off threshold of −1.5 and 1.5 log2-fold change in gene expression (i.e., more than 2.8-fold difference) and a stringent statistical significance threshold of p < 0.001.
Using a stringent staining paradigm, serially adjacent 7 µm sections containing substantia nigra were processed with H&E (Figure 2A), an antibody against total Elk-1 (Figures 2B), and an antibody against alpha-synuclein (Figure 2C).
We were able to detect a high proportion of the training set (87% correctly labeled training site nucleotides) at a stringent j value of 0.01, and up to 92% correctly-labeled nucleotides with j> = 0.04 (Figure 2B).
To confirm that the binding sequence results were not dependent on the particulars of the thresholds chosen, we chose a stringent threshold of 10.6 for the enrichment scores as well as a more lenient value of 10.0 (Supplemental Figure 4).
We performed a stringent analysis that identified 305 probes (FDR<0.14%) and a less stringent analysis that identified 2,313 probes (FDR<2.67%) (Figure S5).
Of course this is a stringent view.
