What statistical test does DESeq use?
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6.8 years ago
pmanga ▴ 60

I was wondering what statistical test does DEseq use for estimating the differential expression values is it a chi-sq. / Fisher exact test or some other?

RNA-Seq Forum • 7.6k views
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That's fine! I did but I am not a statistics person and was a bit confused!

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6.8 years ago
Ying W ★ 4.1k

Where to start.... The simplest answer is "some other"

If you are not satisfied with this answer, I would first try reading the paper though it might be hard to understand so it could be easier to start with a review.

You can think of what DESeq does as kind of like a modified t-test on counts but the counts need to be normalized before you can use them. Istvan's answer here provides a great starting point: Does FPKM scale incorrectly in case of unequal mapping rates? as well as this post

Assuming you have a good  understanding of NGS count data, you should also learn how linear modeling work. The user guide here is great for walking a beginner through how differential expression analysis works. edgeR is a tool similar to DESeq though there are some differences.

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 I am actually using the Jmp Genomics to analyze a KDMM normalized data set, but along the way also performed it with DESeq, I read the paper but wasn't that clear on the exact DE estimation method of DESeq. This should be helpful thanks ...

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I just dug through and saw your post: DESeq statistical test. I agree with what @Devon Ryan says and I'm not quite sure why you opted for KDMM (other than maybe its an option in Jmp?). You might also want to have a look at this thread

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