Question: edgeR, DE between 4 different samples
gravatar for wendy_11
2.3 years ago by
wendy_110 wrote:


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.


ADD COMMENTlink modified 2.3 years ago by James W. MacDonald46k • written 2.3 years ago by wendy_110

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 REPLYlink modified 2.3 years ago • written 2.3 years ago by Aaron Lun20k
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