Check for variation between two replicates in transcriptome data

Question

[sagardesai91]

Hello everyone, I have two control samples for an RNA-seq experiment that are behaving very differently, on doing a PCA, they cluster quite far away from each other. I want to check for variation between the two samples. Could anyone suggest an appropriate statistical test or a package that could help me with the above? Would z-test do?

[ATpoint]

Pearson Correlation is a good start, so cor on the count matrix. What question do you eventually want to answer?

[sagardesai91]

Great! I'll try it out, thanks a lot!

[sagardesai91]

I just want to know how different these two replicates are from each other