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I was wondering if anyone had any advice on comparing two groups where the variance in once group is high and the variance in the other group is low.

Specifically, I am attempting differential gene expression analysis using EdgeR. I have been using the glmLRT function however while playing with other functions I discovered the BCV was 0.79. My understanding is that using a generalised linear model is probably not a valid method to compare these two groups (each with 5 replicates). Can anyone offer advice?

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So you have two groups, small sample sizes and different variances? What is the ratio between sample variances? You can find some advice from this list.

I would guess the distributions are far from normal too? I would maybe try some permutation test, some advice in this list.

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