Expression plot of GoI using EdgeR

Question

[Satyajeet Khare]

Biostars,

The question is perhaps too naive, but I was wondering if there are tools to plot expression of specific gene of interest in EdgeR. I think there are some tools in DESeq such as plotCounts, but I could not find parallel in EdgeR.

Is there any?

Best,

[Sej Modha]

Glimma would be one option that can generate interactive gene expression plots and it is also compatible with edgeR.

Answer 1

[Kevin Blighe]

Just do a simple boxplot with a formula:

boxplot(geneX ~ Condition)

..or use ggplot2: A: Boxplot in ggplot2

[Satyajeet Khare]

Thanks a lot, @Sej and @Kevin. Glimma needs R to be updated. I'll just check if that wont affect my installed packages. Will try ggplot2.