How are gene-level benchmark doses (BMDs) calculated?

Gene-level BMDs are calculated using six steps:

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