Multiple samples using cuffdiff

Question

[tw30282]

Hello,

I was trying to comparing multiple RNA-Seq samples using cuffdiff. However, it is difficult to visualize the FPKM and log2 fold change output file. For example, I have 3 samples A, B, and C. When I look at gene X, I have 3 rows listing the results of A vs B, B vs C, and A vs C.

Is there a way to merge that 3 rows into 1? A vs B vs C? Or which software can achieve that?

Thanks, Tianming

Answer 1

[Istvan Albert]

Cuffdiff performs pairwise comparisons and you can't merge these independent results into a single comparison. You would need a different approach that relies on some kind of statistical model and then perform a test on whether the data follows that model. Accomplishing this is more complicated and I would recommend contacting a statistician.