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Fig. 2 | Cell Regeneration

Fig. 2

From: Comparison of Scanpy-based algorithms to remove the batch effect from single-cell RNA-seq data

Fig. 2

Batch-correction results for multiple tissues from MCA and TM. a, The t-SNE plots present the degree of the batch effect from the MCA multitissue data (containing 26 experimental batches of 23 tissues) before correction (baseline) and after correction using four methods (Regress_Out, ComBat, Scanorama and MNN_Correct). b, c, ASW_batch (boxplot) and the kBET rejection rate (line chart) evaluate the batch-correction effect in the MCA multitissue data. d, The t-SNE plots present the degree of the batch effect from the TM multitissue data (containing 28 experimental batches of 12 tissues) before correction (baseline) and after correction using the four methods (Regress_Out, ComBat, Scanorama and MNN_Correct). e, f, ASW_batch (boxplot) and the kBET rejection rate (line chart) evaluate the batch-correction effect in the TM multitissue data. **pā€‰<ā€‰0.01, ***pā€‰<ā€‰0.001; the Wilcoxon signed-rank test with Benjamini and Hochberg correction was performed between each of the four postcorrection groups and the baseline group

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