I am trying to correlate a continuous physiological trait with gene expression from RNA-seq, particularly trying to identify genes associated with a change in a trait between 2 treatments (n = 5 per treatment). I've already ran standard differential expression analysis but have trait+expression data for each individual so thought could be interesting to attempt correlations. From literature, I've seen linear regressions used, using counts data for each gene as explanatory variable and trait as a response variable.
So my question is how to best incorporate multiple treatments using this approach?
regression of genes and trait data in each treatment separately? then afterwards compare/contrast genes that correlate with the trait in each treatment
regression of genes and traits for both treatments together in same analysis? For this I have seen studies transform physiological trait values for the experimental condition to a measure of difference from the control group.
Any advice/alternate suggestions welcomed. Thanks.