New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
Fig 1
Example of the exploration of batch effects.
Four plots generated by ComBat to correct for batch effects. For the left panel plots, the red lines are the parametric estimates, and the black lines are the kernel estimates for the distribution of effects across genes. The right panel shows Q-Q plots with the red line for the parametric estimate and the ordered batch effects for each gene (black points). The bottom plots show the analyses for the variances and the top plots refers to the means. Plots were generated for batches TSS E9 and E2 to avoid batches containing only one sample.