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Add option to bias-correct GEE variance-covariance matrix for small samples #197

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jr-leary7 opened this issue Sep 19, 2024 · 0 comments
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enhancement New feature or request GEE related to the GEE model backend

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  • as per Li and Redden (2014), using the standard sandwich variance-covariance matrix to perform a Wald test of significance - as we do in waldtestGEE() - leads to inflated Type I error (false positive) rates when the number of subjects is small and / or the number of timepoints per-subject is large
  • this was seen in our simulation study, where we observed high numbers of false positives when using $n_s = 6$ subjects
  • scRNA-seq datasets quite often have low numbers of subjects compared to observations per-subject, making this a problem for the GEE mode
  • several small-sample bias corrections exist, the easiest of which to implement is the DF correction, where $p$ is the number of covariates:

$$ \mathbf{V}_{df} = \left(\frac{n_s}{n_s-p}\right) \mathbf{V} $$

  • thus, it makes sense to add an option to bias-correct the estimated sandwich variance-covariance matrix when the number of subjects is lower than some heuristic threshold e.g., $n_s = 30$
@jr-leary7 jr-leary7 added enhancement New feature or request GEE related to the GEE model backend labels Sep 19, 2024
@jr-leary7 jr-leary7 self-assigned this Sep 19, 2024
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enhancement New feature or request GEE related to the GEE model backend
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