Entering edit mode
3.4 years ago
RNAseqer
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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.
May I ask what the final analysis goal is?
To determine which genes have statistically significant unequal variance between disease and controls.
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).