Correlating Bulk Differential Expression with quantitative

Question

[Nicholas]

Hello everyone,

TL;DR I have bulk RNA-seq data from two groups -- treatment and no treatment, that I would like to correlate with a disease scale. What kind of statistical model would be useful for doing that?

Longer story: There is previous evidence showing a particular disease is associated with another disease. I want to know whether disease A predisposes an individual towards disease B or whether disease A is itself caused by disease B. Basically, I'm hoping to determine the mechanism and directionality of effect using bulk RNA-seq data from individuals with and without disease A who all have varying scales of disease B.

Thank you all so much for any insight!

Nicholas

[Qroid]

You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#multi-factor-designs When specifying the design, instead of ~condition you can use ~condition + disease_scale.

[Nicholas]

Thank you! I will give it a shot