Hi all, hi Mike, we have done RNA sequencing of patient tissues and done the usual analyses including DESeq2 and WGCNA. We have several clinical parameters that we would like to go in depth on, and a correlation with expression of sorts would be helpful. The question is:

For a continuous parameters (imagine cytokine levels or clinical ranking), can a correlation be run on the normalised counts of any given gene of interest across all patients/controls? Would the output of varianceStabilizingTransformation be suitable for this task, e.g., via the output data of plotCounts for the gene of interest?

Thanks, and kind regards, Sebastian

Yes examining the correlation of some continuous variables with the output of the VST is fine.

If you want to test the association, putting the continuous values in the GLM design formula will take into account the count nature of the expression values.