Exact(4)
Both the NOTCH1 and NOTCH4 receptors contain DMRs in the continuous and extreme data sets (Fig. 5e,f).
Second, the Pathd8 software has been introduced as especially suited for large datasets, being only less precise compared with penalized likelihood methods, but giving more sensible answers for extreme data sets.
Then, we identified 234, 685 and 4405 significant DMRs in the children, continuous age and extreme data sets, respectively [FDR < 5%, filtering regions containing probes found to cross-hybridize by (Chen et al., 2013)] (Fig. 2).
As the four new data sets overlapped with the age range of the continuous and extreme data sets, but not of the children data set, we compared the 444 DMRs mapping to 403 genes common to the former two and not found in the latter.
Similar(56)
Interestingly, DMRs in both the children and continuous age data sets are also mostly found within the extreme data set.
The extreme data set also had a significant DMR in the first exon of the shorter variant (Fig. 5a).
For such an extreme data set, it is unlikely that any reasonable objective function would assign an optimal score to the biologically correct alignment.
Table S6 (Supporting information) uses an example of a two-group test for differential methylation by age in the extreme data set.
We found 1338 DMRs that were different between the paired cases and controls in the breast cancer data set, and we compared this DMR list with each of the age-related DMR lists identified earlier (i.e. children, continuous and extreme age data sets).
For instance, we found a much larger number of DMRs in the extreme age data set.
The use of robust regression methods allows reduction of the contribution of extreme data points in a data set.
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