Combined analysis of the initial and replication cohort increased the strength of the association (p = 4.84×10−6).
Genes with the most reproducible differential expression were identified by selecting genes in the initial and replication data sets with Log2FC≥1 and P≤0.05, and then assessing the combined statistical significance using the Fisher's combined P method [29].
Based on the expression of 22,000 genes, a p value<0.05, a false discovery rate of 10%, and fold change of 2 (Log2 ratio of 1), with a standard deviation of 0.3, a sample size of 3 subjects per group gives 80% power in each the initial and replication cohorts [30].
To assure that the results were reproducible, we enrolled the subjects into initial and replication cohorts to identify genes with consistent differences in gene expression, and used a second method to identify differences in gene expression based on the false discovery rate.
When the analysis was separated by initial and replication tests, neither showed significant results (P = 0.086 and 0.058, allele model) (Supplementary Tables 2 and 3).
A concerted effort by researchers and journal editors should also be made to ensure that negative initial and replication studies are published to reduce the impact of publication bias.
a combination of initial finding and replication (when available) in the cited study; effects from minor allele.
The homogeneity test between the ORs of the initial and the replication samples revealed no significant differences.
Initial relative fitness and replication efficiency were determined for both viruses in the MT4 and C8166 T-cell lines (Table 1 and Supplemental Figure S1), which indicates that viral population size and expansion were similar between cellular environments.
For instance, the authors contrast two simple models of replication, stamping machine where the progeny is one generation away from the initial and the geometric replication model where several rounds of replication occur within a single cell.
