I have paired gene expression data before and after a treatment, as well as an ordinal response variable with 3 levels for each sample after treatment. I am interested in the correlation of the (change in expression of 30 genes before and after) with the (response variable), as well as the significance of this correlation. What is the best tool/test to do this? Can it be done in limma?
Since your question is: "correlation of the (change in expression of 30 genes before and after) with the (response variable)", one way could be linear modelling with following code in R:
where resp1_3 is response variable and ge_post_pre_diff is difference of gene expressions (post-pre).
Also why not simple correlation:
cor.test(resp1_3, ge_post_pre_diff, method='spearman')
A scatterplot and boxplot between these 2 variables could also give some insight.
You could post the results of these for further suggestions from others.