The genotype means were estimated using a linear mixed model that considered replications and blocks within replications as random effects while the genotypes were considered as fixed effect.
In the model, we considered replications and blocks within replications as fixed effects and genotypes as random effects.
CDKN1A rs776246 and CDC2 rs2448343 were associated with risk in one population each (MAL and OPS, respectively), but the risk estimates were in the opposite direction to that found in the discovery set and not considered replications.
Most studies consider replication of the whole relation or its horizontal part.
A large graph is divided into several fragments, each of which is resident at one site (we do not consider replication at this point).
Then, considering replication logic and the circumstances at the research sites, Tables 7 and 8 in Appendix reveals, first, the evidence of administrative HRD as a possible configuration (Part 1: Cases D and E), followed by evidence from the rival pattern of strategic HRD (Part 2: Cases A and B).
This is included in Anna's response (4.Shrimp.C), but Beth does not consider replication of treatment (4.Shrimp.D.ii; Table 2, area of difficulty 4h).
We observed that SMAs tend to be of higher significance among CpGs at known imprinted genes compared to non-imprinted genes (Spearman correlation 0.025, p = 4.0E−04 considering discovery p values; 0.019, p = 8.0E−03 considering replication p values).
She raised issues for design and analysis such as understanding the quality of the reference genome for alignment and accounting for the compositional nature of RNAseq samples (considering replication, treatment, organism tissues).
The main conclusion is that to improve the measurement reliability, care should be taken to consider replications and matrix removal prior to sample preparation.
