Question: Multiple samples using cuffdiff
gravatar for tw30282
3.7 years ago by
tw3028210 wrote:


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

ADD COMMENTlink modified 3.5 years ago by Istvan Albert ♦♦ 85k • written 3.7 years ago by tw3028210
gravatar for Istvan Albert
3.5 years ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

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.

ADD COMMENTlink written 3.5 years ago by Istvan Albert ♦♦ 85k
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