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
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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
~conditionyou can use~condition + disease_scale.Thank you! I will give it a shot