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Question: What is difference between classic and GLM edgeR
0
3.5 years ago by
Australia
adrianna-christina0 wrote:

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?

Thank you for your reply

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modified 3.5 years ago • written 3.5 years ago by adrianna-christina0
1
3.5 years ago by
United States
James W. MacDonald47k 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.

ADD COMMENTlink written 3.5 years ago by James W. MacDonald47k
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 3.5 years ago • written 3.5 years ago by Aaron Lun20k
0
3.5 years ago by
Australia
adrianna-christina0 wrote:

Thanks a lot James and Aaron!!

ADD COMMENTlink written 3.5 years ago by adrianna-christina0
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