Differential expression evaluated by rank_genes_groups using t-test vs. wilcoxon method

theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

https://arxiv.org/abs/2204.13545

MIT License

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Differential expression evaluated by rank_genes_groups using t-test vs. wilcoxon method #164

Open ceesu opened 7 months ago

ceesu commented 7 months ago

Hello, thank you for sharing the code for your model.

I noticed that in calculating differential expression, the model calls sc.tl.rank_genes_groups with the default method in helper.py. It seems the default method would be using t-test.

One of the methods compared in the paper, scGen, also calls sc.tl.rank_genes_groups but specifying the method to be wilcoxon.

I was wondering could you say more about the differences? Thanks,