Fig. 1. Batch effects impact both gene expression and splicing analysis.

Uniform manifold approximation and projection (UMAP) of gene expression analyses (a, c) and splicing analysis (b, d) for TARGET (top, N = 870) and ENCODE (bottom, N = 489). Colors indicate batch identity. Numbers in red represent percent of total variation (R²) associated with batch in each dataset. Shapes mark samples from the same patient (TARGET, patient TARGET-10-PANKAK) or experiment type (ENCODE, U2AF2 KD) which cluster by batch. TPM, transcripts per million; FC, Fold change; dPSI, delta percent splice inclusion.