Fig. 1
From: Alternative empirical Bayes models for adjusting for batch effects in genomic studies
Distribution of sample-wise mean and variance estimates from each batch in the bladder cancer data. Estimates are calculated within each sample as previously described. a Boxplots of sample-wise mean estimates (\(\bar {\gamma }_{ij}\), as in Eq. (3)) within each batch. The sample-wise mean estimates for batch 2 in the unadjusted data are significantly different from the other batches. Both mean-only and mean/variance ComBat adequately correct this batch 2 mean difference. b Boxplots of sample-wise variance estimates across batches. The sample-wise variance estimates are not significantly different in the unadjusted data. Adjusting either just the mean or both mean and variance does not makes the estimates more similarly distributed, meaning that adjusting the variance is not necessary