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It should be noted that in the estimation of confidence limits for translation rates, the protein half-life dataset was assumed not to have a significant location error.
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In order to evaluate the performance of the different methods, we now run a simulation where parameters obtained from the Iris dataset are assumed to be the "true model".
The results of TF on this dataset are assumed to be accurate.
Missing continuous infusion durations (for two occasions in the model development dataset) were assumed to be 16 h, per protocol.
One dataset is assumed to correspond to one inferred GRN topology, and all inferred GRNs should share the same network topology as their corresponding datasets are generated from the same underlying gene network.
Expression levels and half-lives in this dataset were assumed to be identical for all entries, but were allowed to vary randomly around the true value in a lognormal distribution with variances similar to those estimated for the observed error in the real genome-wide datasets.
7 The FDA dataset is assumed to be an unbiased (but not the complete) body of evidence in the specialty of antidepressants and so is regarded a gold standard data source owing to the legal requirements of submitting evidence in its entirety to the FDA and its careful monitoring for deviations from protocol.
The BLASTp RBH between the GRS and CCDS datasets was assumed to be robust and so if a contig was wrongly assigned to a CCDS (via the GRS dataset), it is likely that BLASTx is the source of error.
However, all the datasets are assumed to be subject to the same selective reporting bias, i.e. the parameters w = (w1,.., wk) are the same for all datasets.
These datasets were assumed to be representative of standard qPCR data because they are included as example datasets in the qpcR package for the purpose of demonstrating various model-fitting procedures for quantification of qPCR data.
In fixed effects models, the true effect of risk allele is assumed to be the same value in each dataset, whereas in random effects models the risk allele effects for the individual datasets are assumed to vary around some overall average effect.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com