apply Kruskall or other non-parametric test for multiple comparisons

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bhgyu ▴ 30

@bhgyu-13069

Last seen 6.4 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 • 1.6k views

ADD COMMENT • link 7.1 years ago bhgyu ▴ 30

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Why do you want a non-parametric test?

ADD REPLY • link 7.1 years ago chris86 ▴ 420

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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.

ADD REPLY • link 7.1 years ago bhgyu ▴ 30

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

ADD REPLY • link 7.1 years ago chris86 ▴ 420

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