From: PCA outperforms popular hidden variable inference methods for molecular QTL mapping
Inference method | Method | Response, covariates | Method abbr. (if selected) | |
---|---|---|---|---|
(A) | (B) | (C) | (D) | |
1 | Ideal | Y, \(X_1\) + \(X_2\) | Ideal | |
2 | Unadjusted | Y, \(X_1\) | Unadjusted | |
3 | PCA_direct | PCA_direct_screeK | Y, \(X_1\) (filtered) + top PCs | PCA |
4 | PCA_resid | PCA_resid_screeK | Y, \(X_1\) + top PCs | |
5 | SVA_trueK | SVA_trueK | Y, \(X_1\) + SVs | |
6 | SVA_BE | SVA_BE | Y, \(X_1\) + SVs | SVA |
7 | PEER_noCov_trueK | PEER_noCov_trueK_factors | Y, \(X_1\) (filtered) + PEER factors | |
8 | PEER_noCov_trueK | PEER_noCov_trueK_residuals | \(Y_\text {resid}\,\), NULL | |
9 | PEER_noCov_largeK | PEER_noCov_largeK_factors | Y, \(X_1\) (filtered) + PEER factors | |
10 | PEER_noCov_largeK | PEER_noCov_largeK_residuals | \(Y_\text {resid}\,\), NULL | |
11 | PEER_withCov_trueK | PEER_withCov_trueK_factors | Y, \(X_1\) + PEER factors | PEER, true K, factors |
12 | PEER_withCov_trueK | PEER_withCov_trueK_residuals | \(Y_\text {resid}\,\), NULL | |
13 | PEER_withCov_largeK | PEER_withCov_largeK_factors | Y, \(X_1\) + PEER factors | |
14 | PEER_withCov_largeK | PEER_withCov_largeK_residuals | \(Y_\text {resid}\,\), NULL | PEER, large K, residuals |
15 | HCP_trueK | HCP_trueK | Y, \(X_1\) + HCPs | HCP |