I analysed samples(two replicates for each group) with overexpression of my interest, I find that overexpression is successful compared from OE to control, but all q_value comes out from cuffdiff are higher than 0.05 and shows no significance including the overexpression gene. which FPKM differs from 26 in control to 3200 in OE. How come this result could be caused? Is p_value significant for analysis?
The test statistic will explain why the data was not considered significant. The other values describe this metric. All is explained here: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#differential-expression-tests
Galaxy tutorials for RNA-seq: https://galaxyproject.org/learn/
Thanks, Jen, Galaxy team