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Mann-Whitney test -- is it applicable to compare log2 fold change in a subset of genes to all genes?

Subj. Mann-Whitney test -- is it applicable to compare log2 fold change in a subset of genes to all genes?

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rna-seq
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written by biostart biostart

How big are the subsets and full sets? You likely want GSEA instead...

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written by Devon Ryan Devon Ryan

The full set is 7,000 genes, and the subsets are like 1,000, 2,000 genes

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written by biostart biostart

N.B., you'll need abs(log2 fold change) for Mann-Whitney to make sense.

With a subset of that size the question becomes how you want to think about the comparison. Given your background question, I suspect that GSEA is answering the question you want to ask (i.e., "given two groups, is the subset 'perturbed' in one group versus the other in respect to the other genes").

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written by Devon Ryan Devon Ryan

Hmm, if I take abs(log2 fold change), then how do I distinguish between up- and downregulated? This will be a problem... But what if I just use the two sample t-test, would that be problematic?

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written by biostart biostart

You're comparing a subset versus the whole. The direction of change of individual genes is completely irrelevant to that question.

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written by Devon Ryan Devon Ryan

I actually don't understand the argument about "abs". Why negative values are a problem for Mann-Whitney?

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written by biostart biostart

I just need one quick calculation, would not want install GSEA for that. Do you know, which statistical test would be used in GSEA in this case?

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written by biostart biostart

It's largely a more complicated version of ks.test() in R.

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written by Devon Ryan Devon Ryan

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