Question: ballgown: how to test for DE for my experimental setup
gravatar for michael
4 weeks ago by
michael0 wrote:

I have the following setup for my rna-seq experiment:

5 samples Control 5 samples 1x concentration of chemical compound 5 samples 10x concentration of chemical compound

My workflow is Hisat2 > Stringtie > ballgown

Now, for ballgown "stattest", how would you test considering my experimental setup. I would just do two tests "control vs 1x" and "control vs 10x". But I guess to analyse all three conditions in one statistical test would be better. Is there a way to do this using ballgown?

rna-seq ballgown • 28 views
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