Hi, I have two Rna-Seq datasets and I have determined the differentially expressed genes in those 2 datasets. I intersected the dataset to find the genes that is common to both datasets. I want to compare the genes that is upregulated in one of the dataset but downregulated in the other dataset and vice versa. What's the best metric for doing the comparison(logCPM, log2FC, RPKM/FPKM, Z-score) and how would I display the results in a graph/figure. I have around 700 common genes.

Thanks!

Your question is off-topic for this support site, which is meant to help people with technical questions for Bioconductor packages. You might instead try over on biostars.org.

My favourite method is simply to plot log2FC from the first dataset vs log2FC for the same genes from the second dataset. This plot clearly displays genes that have opposing log2FC responses in the different datasets.