Hi, I am analyzing a time-course experiment and I am using the "LRT" test as I am interested in changes at any time point throughout the experiment. I would like to visualize this perhaps by using a Volcano plot to "show" the changes between the first day of the experiment and the last; however, I know that I can't use the fold changes associated with the "LRT" test as they are not directly associated with the actual hypothesis test, so is it okay to use the Wald test for this visualization purpose and color only significant genes that were found with padj < 0.05% in the
results(dds_lrt)? Is there a better way to visualize the "LRT" results?
dds_lrt <- DESeq(dds_lrt, test="LRT", reduced = ~ 1) res_lrt <- results(dds_lrt)