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Several cases that were judged to be methylated (i.e., to have a good prognosis) by MSP belonged to clusters 3 and 4. For example, samples 13 and 16 belonged to cluster 4; both showed four months of PFS and were described as poor prognosis [ 2], but were judged to be methylated and to have a good prognosis by MSP.
For example, samples E2 and E9 displayed a pairwise FST value of 0.069 across all loci.
For example, samples G3 and E2 displayed the greatest similarity of any pairwise comparison (Fig. 2), and clearly incorrect assignment was greatest between these two samples.
For example, samples V5 and V7 (marked with arrows), which exhibit a much lower diversity than other control samples, appear to be more closely related to each other and separate from the remaining control samples.
As demonstrated in the current simulation results comparing two groups (for example, samples A and B), the use of default normalization methods implemented in the existing R packages performed poorly in simulations where almost all the DEGs are highly expressed in Sample A (i.e., the case of PA > > 50% when the range is defined as 50% ≤ PA ≤ 100%).
For example, samples s i and s j are defined to be equal if both samples have one or more copies of the minor allele for attribute a, which corresponds to the dominant genetic model at locus a.
The success of such a study depends on multiple factors that influence the range of observable effect sizes (for example, sample size and the magnitude and direction of natural selection) [ 26].
Metaregression is a technique used to explore the relation between study characteristics (for example, sample size and journal of publication) and effect size.
However, in 3/56 statements, the meaning of anonymity (no possibility to link data to a person) and coding was confused (as an example "samples will be anonymized and coded").
