Question: Mann-Whitney test -- is it applicable to compare log2 fold change in a subset of genes to all genes?
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gravatar for biostart
2.5 years ago by
biostart290
Germany
biostart290 wrote:

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 • 1.1k views
ADD COMMENTlink written 2.5 years ago by biostart290

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

ADD REPLYlink written 2.5 years ago by Devon Ryan88k

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

ADD REPLYlink written 2.5 years ago by biostart290
1

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").

ADD REPLYlink written 2.5 years ago by Devon Ryan88k

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?

ADD REPLYlink written 2.5 years ago by biostart290

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

ADD REPLYlink written 2.5 years ago by Devon Ryan88k

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

ADD REPLYlink written 2.5 years ago by biostart290

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?

ADD REPLYlink written 2.5 years ago by biostart290
1

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

ADD REPLYlink written 2.5 years ago by Devon Ryan88k
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