Question

edgeR, DE between 4 different samples

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wendy_11 • 0

@wendy_11-10047

Last seen 8.7 years ago

Hi, I am trying to use edgeR for analysis of gene expression across 4 RNASeq samples(different stations) (3 replicates each. The information I would like to have, is the expression (fold change) for each gene across all 4 stations. If I use the GLM method by selecting one intercept, I will only get for each gene, the fold change in 3 of the 4 stations. How can I retrive the expression (fold change) for the 4th station? Should I use another approach?

Thanks for the help, any suggestion is really appreciated.

Aloha

edger differential gene expression GLM Tutorial • 1.6k views

ADD COMMENT • link updated 8.7 years ago by James W. MacDonald 67k • written 8.7 years ago by wendy_11 • 0

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Entering edit mode

A couple of things:

The "Tutorial" post is meant for people who write tutorials, not for people who are requesting tutorials.
What do you mean when you say you want the fold change across all 4 stations? Fold change relative to what? Between two stations? There is no concept of a fold change for each station in your design, so you need to clarify this.
Show the code you've currently got, so that we can see what you've done.

If you respond to this post, use the "add comment" rather than making a new answer.

ADD REPLY • link 8.7 years ago Aaron Lun ★ 28k