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Old 11-23-2016, 07:17 AM   #1
shanshuiii
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Location: Minnesota

Join Date: Nov 2012
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Default Question: Test fold change significany using duplicate reference transcriptome (RNA-S

Hi, All

I've also posted this on BioStars, sorry for the re-post (https://www.biostars.org/p/223635/)!

Is it possible (or reasonable) to compare a single RNA-Seq sample (without replicate) to a duplicated reference transcriptome?

In our experiment, we have sequenced the control treatment in duplicate, but all the other treatment only once. I was wonder if it is possible to use the duplicate controls as a reference to infer the significance (p-value) of the fold change in other samples?

It seems to me it is a simple t-test, but I'm not sure if it makes sense. Also, is it possible for us to use DESeq(2)?

Thanks!
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