what is the best R package/function to perform an Equality of variance F-test on TMM log2 gene expression values
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3.4 years ago
RNAseqer ▴ 280

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 • 984 views
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May I ask what the final analysis goal is?

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

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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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