DESeq2 R markdown plotting problem

Question

[Pahi]

Hello!

I'm working on my DESeq2 data analysis and I want to make a report with R Markdown. But I have a problem when I get to the deseq2 plotMA part.

In the markdown HTML I get a plot like this:

But when I run the SAME code in R I get a plot like this:

Any idea what could be the problem?

Answer 1

[swbarnes2]

What other libraries are you loading? My guess is on your markdown, plotma is being called from some other library. You can make sure that your can specify that you want deseq2::plotma

[Pahi]

Yes! Thank you! That solves the probelm!