Question

tximport + edgeR not recommended?

0

Entering edit mode

simon.michaelis88 • 0

@simonmichaelis88-23794

Last seen 4.5 years ago

I was reading blog posts, manuals and tutorials to find a good DEG pipeline. I thought edgeR was a good choice and tximport was good to summarise my transcript level abundances, but then I saw this tweet from a well-known PI who claims that this was a terrible choice. Is edgeR + tximport not reliable?

Link to tweet

tximport edgeR • 1.3k views

ADD COMMENT • link updated 4.5 years ago by Michael Love 43k • written 4.5 years ago by simon.michaelis88 • 0

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Oh, Lior. Looks like he's just trying to pick a fight there. What does he think will happen, that we'll read it and go, "Gosh, Lior's right, we better retire edgeR"? Probably best to take tweets with a grain of salt.

ADD REPLY • link 4.5 years ago Aaron Lun ★ 28k

score 3 · Answer 1 · 2020-07-03

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Michael Love 43k

@mikelove

Last seen 5 days ago

United States

We published a systematic assessment of DE methods downstream of tximport, in particular across a variety of sample sizes, and found edgeR to be one of the best performing methods. Click through on the image to the DGE section.

ADD COMMENT • link 4.5 years ago Michael Love 43k