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bioRxiv · 10.1101/463265

Towards a post-clustering test for differential expression

Zhang, J. M.·Kamath, G. M.·Tse, D. N.
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Abstract

Single-cell computational pipelines involve two critical steps: organizing cells (clustering) and identifying the markers driving this organization (differential expression analysis). State-of-the-art pipelines perform differential analysis after clustering on the same dataset. We observe that because clustering forces separation, reusing the same dataset generates artificially low p-values and hence false discoveries. We introduce a valid post-clustering differential analysis framework which corrects for this problem. We provide software at https://github.com/jessemzhang/tn_test.

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Zhang, J. M., Kamath, G. M., Tse, D. N.. 2018-11-05. Towards a post-clustering test for differential expression. https://doi.org/10.1101/463265

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