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DESeq2 R markdown plotting problem

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:

enter image description here

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

enter image description here

Any idea what could be the problem?

markdown r plot deseq2
• 1,398 views • link
written by Pahi • Pahi

1 answer

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

• 0 views • link
written by swbarnes2 swbarnes2

Yes! Thank you! That solves the probelm!

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written by Pahi • Pahi

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