Question: Why DE genes are not among highly variable genes between groups
gravatar for Björn
23 months ago by
Björn40 wrote:

I got list of "highly variable genes" between Groups A x B using variance in edgeR (ref: highly variable genes) Then performed standard edgeR analysis to find DE genes. ref: edgeR

PROBLEM: Why none of the DE genes between A x B are included in "highly variable genes"

My questions 1. What is the reason for the problem ? 2. Considering the problem, what is the use of "highly variable genes" in publication ? Can I simply exclude it and go with DE gene analysis only.

mirna edger variance • 1.4k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 23 months ago by Björn40

did you determine your "highly variable genes" as it is indicated in your first reference? If so, these are not highly variable genes between groups A and B, as you call them, but rather genes with the highest variance in your data. That means they can change a lot independently of the group. For this reason you shouldn't expect an overlap with your AvsB DEGs.

ADD REPLYlink written 23 months ago by Martombo2.6k
gravatar for Devon Ryan
23 months ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

Highly variable genes are useful for clustering samples and seeing if you've done things like swapped a sample label or have outlier samples. One should not expect them to be differentially expressed. You're looking at a quality control step, how you proceed will depend entirely on what it looks like.

ADD COMMENTlink written 23 months ago by Devon Ryan94k
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