Co-variants in differential expression analysis

Question

[Ati]

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

[Devon Ryan]

What have you tried? The edgeR and limma user manuals are pretty good, have you read through them?

[Ati]

Yes I have read them. But I am not sure, how to define co-variants! do have any example?

[Devon Ryan]

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.

[Ati]

Thanks in advance for the nice point

[Irsan]

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.

[mark.ziemann]

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.