apply Kruskall or other non-parametric test for multiple comparisons
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bhgyu ▴ 30
@bhgyu-13069
Last seen 4.6 years ago

Hello there,

I've been struggling to find a non-parametric test to determine significantly differentially expressed genes in sample sets with lots of features.

Running Wilcox etc always gives me the same p-value even if I do something like:

ttest <- apply(dataset, 2, kruskal.test)

Does anyone know how to determine top features non-parametrically?

Cheers!

r kruskal ttest nonparametric • 983 views
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Why do you want a non-parametric test?

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Hi Chris, cause I'm dealing with very small n of samples and can't be certain conditions for parametric tests are met.

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I'd just use limma or one of the other bioconductor packages like DESEQ2.