I am comparing 2 treatment conditions and want to see the graphs of same clusters (having same patterns) from 2 treatments.
I am using log2 normalized counts. Data in one sample ranges from -6 to 6 and -10 to 10 in second. I was wondering on "how to plot the two clusters in same scale? i.e both ranging from -10 to 10.
Moreover I have already separated the clusters with my codes in to different classes like UU ( Up regulated in both conditions, DU, UD …… but when I use MeV the number of genes is different in different groups and clusters are not well defined. What parameters I should try? I am using QT with Pearson Cor and number of clusters = 8 (max possible combinations).
Thanks in advance