First of all, we start pooling pairs of artificial datasets, and thereafter increase the number of pooled datasets pooled until all six artificial datasets are pooled.
Based on either the datasets pooled from all four populations, or the datasets of individual populations, positive selection was indicated by some demographic models in the Fay and Wu's H test, which takes the ancestral status of polymorphism sites into consideration and is sensitive to an excess of derived alleles.
Results are based on 100 imputed datasets pooled using Rubin's rule [22].
After ten iterations for each of the five imputation datasets, pooled estimates were used for all subsequent analyses below.
We hypothesize that a significant association exists between the classification error and the number of datasets pooled.
For the breast cancer samples, analyses were performed both within each individual dataset and across the aggregated dataset derived from all individual datasets pooled together, as indicated.
However, in many empirical datasets, pooled samples have a lower Tajima's D than local samples (e.g. Ptak and Przeworski 2002).
In addition, we evaluated the performance of each classifier on a seventh independent dataset (Vijver et al. [ 3]). Figure 6A and 6B show the DLCV error and validation error as a function of the number of datasets pooled.
These results indicate a positive trend in the number of datasets pooled and the number of genes selected in the signatures (Pearson correlation of 0.38 with p = 1.9 e - 3).
The main sources of performance improvement are due to the following: (i) non-linear modeling and advantage over linear PWM models (Obenauer et al., 2003), (ii) balanced discriminative training and (iii) datasets pooling.
The wild dataset pools various collections made from 1999 to 2005 covering all months of the year.
