Gene-level BMDs are calculated using six steps:
- Multiple statistical models are fit to the gene expression values for each gene
- The model fits are filtered to remove poor fits using the lack-of-fit p-value
- From the remaining fits, the best-fit model for each gene is selected, thus different genes can have different best-fit models
- Benchmark responses are computed for each gene based on the expression of the control samples
- The BMD is calculated as the dose that corresponds to the benchmark response
- BMDs are filtered to remove those with low confidence