GEO series | Exp. design (group vs batch) | Design bias (Plow vs group) | Kruskal Wallis’s P-value (batch vs Plow) | Batch effect on base PCA | Batch effect removed after batch correction | Batch effect removed after Plow correction | Plow performance compared to batch | Plow performance with outlier removal | Performance of combined correction |
---|---|---|---|---|---|---|---|---|---|
GSE120099 | Good | 0.655 | 4.24E−03 | Yes | Yes | No | Worse | Worse | Worse |
GSE117970 | Poor | 0.608 | 8.41E−04 | Yes | No | Yes | Better | Better | Worse |
GSE163857 | Poor | 0.522 | 2.09E−02 | No | – | – | Comparable | Comparable | Worse |
GSE162760 | Good | 0.496 | 2.36E−12 | Yes | Yes | Yes | Comparable | Better | Comparabe |
GSE182440 | Very good | 0.495 | 1.06E−01 | No | – | – | Comparable | Better | Better |
GSE144736 | Poor | 0.494 | 3.63E−01 | Yes | Yes | No | Comparable | Better | Worse |
GSE82177 | Very good | 0.493 | 5.75E−01 | Yes | Yes | No | Comparable | Better | Better |
GSE171343 | Very good | 0.488 | 8.25E−02 | Yes | Yes | No | Comparable | Comparable | Comparable |
GSE173078 | Very good | 0.479 | 2.93E−07 | No | – | – | Comparable | Comparable | Comparable |
GSE61491 | Good | 0.448 | 2.13E−01 | Yes | Yes | No | Comparable | Comparable | Better |
GSE163214 | Good | 0.443 | 1.03E−02 | Yes | Yes | Yes | Comparable | Comparable | Better |
GSE153380 | Poor | 0.442 | 1.58E−01 | No | – | – | Comparable | Better | Better |