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The absolute value of the difference between the replicated sample size calculation and the authors' target sample size was greater than 10% for 47 articles (30%) and greater than 50% for 10 (6%).
A stepwise procedure, using thresholds of p=0.05 for variable selection and elimination, was applied to each replicated sample, and only the risk factors selected in at least 50% of the procedures were included in the conditional logistic regression models as confounders.
One unique copy of each replicated sample was included in the analysis, preferentially retaining the sample with the higher genotyping call rate.
Overall, 73 articles (34%) reported enough parameters for us to replicate the sample size calculation, had an accurate calculation (the replicated sample size calculation differed by less than 10% from the reported target sample size), and had accurate assumptions for the control group (the differences between the a priori assumptions and their estimates was less than 30%) (fig 5).
A stepwise regression was performed in each replicated sample with thresholds of p = 0.05 for variable selection and for variable elimination [ 19].
Within-assay precision for a replicated sample on the same plate (%CV of intra-assay variation) for a selected sample was < 6%.
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In this study, five replicated samples were used from each treated and untreated sample.
CIs were computed as bootstrap 95% percentile intervals based on 10000 replicated samples.
The calculated error rate was approximately 3% based on negative controls and replicated samples.
This exceeds previously published metatranscriptomic studies because of the inclusion of replicated samples.
All the replicated samples exhibited identical results.
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