In our case, we sampled candidates using Gaussian distributions around the current estimate θ k), decreasing the variance when k increases.
Owing to the low value of cryptic gene flow (0.025 = 1 – 0.99992), the incorrect assignment of genets within sampled candidates as pollen donors, pollen parents of nearly all examined offspring were identified amongst adult genets within the study area.
DNA was extracted as previously described [54] from either scale samples (candidate parents) or whole tissue (embryos).
For any positive sample candidate, if more than 30% neighbors of this residue are the positive sample candidates, the sample is considered as a positive sample; otherwise, it is considered as a NP & NN sample.
The purpose of step (b) is to sample candidate values of SN and SP that lie between their respective theoretical lower and upper boundaries.
For each residue on the surface, if the distance between any nonhydrogen atom of the residue and any atom of the ligand is less than 7 angstroms, this residue is kept as a positive sample candidate; otherwise, the residue is kept as a negative sample candidate.
The negative sample candidate is defined as negative sample if the average depth value of its neighbors is less than 8 and the number of its neighbors is greater than 5. Figure 3 shows the framework to select the samples.
Using FDR cut offs of ≤ 0.1 and ≤ 0.01, 196 (136 more and 60 less expressed in treated samples) and 30 (28 more and 2 less expressed in treated samples) candidate target genes were found, respectively (Additional file 3: Table S3).
When attempting to identify potentially isomerized peptides in unknown samples, candidate peptides from different LC peaks are selected if they have the same mass and exhibit similar fragmentation patterns.
When the number of potential regulators is large, relevant variables will less likely be sampled as candidates for establishing splitting rules.
