Question: What statistical test does DESeq use?
gravatar for pmanga
5.7 years ago by
United States
pmanga40 wrote:

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 • 5.7k views
ADD COMMENTlink modified 5.7 years ago by Ying W4.0k • written 5.7 years ago by pmanga40

That's fine! I did but I am not a statistics person and was a bit confused!

ADD REPLYlink written 5.7 years ago by pmanga40
gravatar for Ying W
5.7 years ago by
Ying W4.0k
South San Francisco, CA
Ying W4.0k wrote:

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.

ADD COMMENTlink written 5.7 years ago by Ying W4.0k

 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 ...

ADD REPLYlink written 5.7 years ago by pmanga40

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

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Ying W4.0k
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