I want to analysis NGS data from case and control. I want to consider 3 co-variants in this analysis using edgeR and Voom.
Would you please guide me.
Thanks a lot
What have you tried? The edgeR and limma user manuals are pretty good, have you read through them?
Yes I have read them. But I am not sure, how to define co-variants! do have any example?
A covariate is no different from a group, you just don't use a factor.
sampleTable = data.frame(samples=c("samples", "go", "here", ...),
groups=factor(c("group1", "group1", "group2", ...)),
age=c(40, 50, 25, ...))
mm = model.matrix(~groups + age, sampleTable)
age is an example of a covariate above.
Thanks in advance for the nice point
Do you know what you mean with co-variants? If you do, you should really be able to figure it out by reading the edgeR and/or limma vignettes like Devon said.
If you have a count matrix already, you can use the Degust (http://vicbioinformatics.com/degust/index.html) GUI to perform edgeR with a simple case-control design. It also gives you the R code used so you can then customise the analysis.
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