Question: What is difference between classic and GLM edgeR
0
3.9 years ago by
Australia

Hi,

I have a RNA-seq experiment data and I want to extract differentially expressed miRNAs for the data. The data is from two groups(cell type1 and cell type 2; both have biological duplicates) and I want to know which miRNAs are differentially expressed between these two groups.

Which approach of edgeR should I use?

The classic one with exactTest function or the GLM approach. What's the difference between the exactTest and GLM results?

r edger de • 2.4k views
modified 3.9 years ago • written 3.9 years ago by adrianna-christina0
Answer: What is difference between classic and GLM edgeR
1
3.9 years ago by
United States
James W. MacDonald49k wrote:

The edgeR User's manual describes the differences between the two tests, in a relatively heuristic manner, starting on page 5:

http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

But the take-home message is that you should use exactTest() if you only have two groups, and fit a GLM if you have a more complicated design.

1

Of course, the GLM approach will work just fine with the two-group design. Even though exactTest works for such designs, using GLMs has the benefit of allowing access to other functionality within edgeR, e.g., quasi-likelihood methods, fold change testing with TREAT. I generally use the GLM approach as my default, as it means I can avoid having to change my analysis pipeline for new datasets and designs.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Aaron Lun22k
Answer: What is difference between classic and GLM edgeR
0
3.9 years ago by
Australia

Thanks a lot James and Aaron!!