tximport + edgeR not recommended?
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@simonmichaelis88-23794
Last seen 16 months 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 • 331 views
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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.

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@mikelove
Last seen 55 minutes 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.

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