Biostar Beta. Not for public use.
What statistical test does DESeq use?
0
Entering edit mode
5.8 years ago
pmanga • 20
United States

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 • 4.2k views
ADD COMMENTlink
0
Entering edit mode

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

ADD REPLYlink
5
Entering edit mode
16 months ago
Ying W ♦ 3.9k
South San Francisco, CA

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: https://www.biostars.org/p/99689/ 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
0
Entering edit mode

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
0
Entering edit mode

I just dug through and saw your post: previous post. 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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1