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what is the best R package/function to perform an Equality of variance F-test on TMM log2 gene expression values

What is the best R package/function to perform an Equality of variance F-test on TMM log2 gene expression values?

I have a model I want to use:

~ Disease + Age + Alchohol + BMI

And I have my table of TMM normalized log2 gene expression data. I would like to conduct a gene-wise F-test for equality of variance on each gene, and then sort based on FDR corrected pvalues all the significant genes.

I feel like this is a simple task but I am running into problems because there seems to be an embarrassment of riches when it comes to F-tests and Im worried I'll use the wrong one.

gene-expression f-test equality-of-variance
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updated by ATpoint ATpoint • written by RNAseqer RNAseqer

May I ask what the final analysis goal is?

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written by ATpoint ATpoint

To determine which genes have statistically significant unequal variance between disease and controls.

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written by RNAseqer RNAseqer

So essentially differentially expressed genes, is it? Why not just plugging your raw counts into DESeq2/edgeR/limma-voom, or if these log2 normalized counts are all you have plug into limma? This is very common and established while what you seem to do is not (afaict).

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written by ATpoint ATpoint

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