Hi and thanks for reading.
I have the ballgown element with e.ctab, t.ctab, i.ctab, e2t.ctab, i2t.ctab data for 4 samples (2 replicas of mutant and 2 replicas of control).
Well, I'm not able to process the data to make scatterplots and to extract the DE gene list.
I have now 2 variables: results_genes (with fc, pval, qval, mean and ids) and gene_expr (with the FPKM of each sample).
The scatterplot I want to do is one with all genes expressed and then, select and colour the activated genes (fc > 2) and the repressed ones.
How can I get there?