Question

Applicability of AUCell to bulk RNA-seq

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Lucy ▴ 60

@lucy-17014

Last seen 12 days ago

United Kingdom

Hi,

I was wondering whether AUCell can be used to test for gene set enrichment in bulk RNA-seq samples: https://github.com/aertslab/AUCell/issues/38

Moreover, what statistical tests would be suitable for comparing AUCell scores between conditions. Since AUCell scores are rank-based, I presume non-parametric tests would be most applicable?

Best wishes,

Lucy

AUCell AUcell • 705 views

ADD COMMENT • link 9 months ago • updated 8 months ago Lucy ▴ 60

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The problem is that with non-parametric tests using these scores you have low power at typical (low) sample size. Why not just using something like fgsea?

ADD REPLY • link 9 months ago ATpoint ★ 4.0k

score 1 · Answer 1 · 2023-07-25

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

There are any number of packages meant to do gene set enrichment (or other gene set tests) in bulk RNA-Seq data. Why do you want to use something that is meant for scRNA-Seq data?

ADD COMMENT • link 9 months ago James W. MacDonald 65k

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Thank you ATpoint and James W. MacDonald for your responses. A paper I am reviewing has used this approach for bulk RNA-seq data, so I wanted to understand whether this is a statistically valid method or not?

ADD REPLY • link 9 months ago • updated 8 months ago Lucy ▴ 60