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. 2021 Dec 10;24(3):635–652. doi: 10.1093/biostatistics/kxab039

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© The Author 2021. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 1. — Three figures are used to illustrate that ComBat+Cor reduces the exaggerated significance seen when ComBat is applied based on simulated data that mimics the bladderbatch experimental design. Note that the original bladderbatch data has unbalanced group-batch design and small (mean and variance) batch effects. The benchmark approach refers to the approach that applies ordinary differential expression analysis to data without any batch effects. (a) QQ plot of p-values using ComBat and the p-values using the benchmark approach. The line falls above the identity line, suggesting that p-values generated by ComBat concentrate at smaller values than those generated on the data without batch effect. (b) QQ plot of p-values using ComBat+Cor () and p-values using the benchmark approach. (c) line chart comparing the distributions of p-values using ComBat, ComBat+Cor, and the benchmark approach.

Inline graphic — Three figures are used to illustrate that ComBat+Cor reduces the exaggerated significance seen when ComBat is applied based on simulated data that mimics the bladderbatch experimental design. Note that the original bladderbatch data has unbalanced group-batch design and small (mean and variance) batch effects. The benchmark approach refers to the approach that applies ordinary differential expression analysis to data without any batch effects. (a) QQ plot of p-values using ComBat and the p-values using the benchmark approach. The line falls above the identity line, suggesting that p-values generated by ComBat concentrate at smaller values than those generated on the data without batch effect. (b) QQ plot of p-values using ComBat+Cor () and p-values using the benchmark approach. (c) line chart comparing the distributions of p-values using ComBat, ComBat+Cor, and the benchmark approach.