EBSeq & Nested Design

[Pietro Mello]

Hi there,

I've been looking through EBSeq's documentation and I couldn't really figure out if EBSeq can handle nested designs. I have a situation where I am performing comparisons of distinct tissues within and between specimens. Thus, I'm performing two distinct analyses (within and betweeN) and looking for overlaps of DE genes across these two experimental designs. At first I assumed that the model would be default incorporate nestedness based on the way it performs it's hypothesis testing. However, when I ran the program I noticed that in comparison to other software (DEseq2, sleuth and edgeR) it outputs considerably less significantly DE genes for within specimens than between specimens. A pattern that I would observe in the other methods whenever I did not account for this 'nestedness', in this case, specimen i.d. .

Would someone be kind enough to point me towards a way to performing this analysis? Or maybe point me on what I might be doing wrong? I followed the steps for layed out in the EBSeq Vignette, Section 5.1.

Thanks!

P