I have an RNASEQ experiment with 6 samples (3 treatments and 3 corresponding controls, i.e. A,B,C and ctrlA, ctrlB, ctrlC).
I used cuffdiff to determine the differentially expressed genes/isoforms for the 3 comparison: A vs ctrlA, B vs ctrlB, C vs ctrlC and got some sets of interesting genes/isoforms.
When I compute the correlation between the samples and then clustering, I was expecting to see either the treatments clustering with their corresponding control or clustering together but separately from the control. Instead they all have high correlation > 0.98 with each other (treatment and control).
Is it possible to have DE genes among samples that are highly correlated? My first interpretation would be that the genes have a different expression magnitude across samples, but their trend is conserved across sample. Is this correct? What can I do to further test the data?
Thanks in advance