Use padj instead of p-value to ploting DE genes using EnhancedVolcano

Question

[adR]

Hi there, I may ask how to plot EnhancedVolcano using padj instated of P-value?

[Nicolas Rosewick]

What did you try already ?

Answer 1

[Kevin Blighe]

Hi, I developed EnhancedVolcano. You just need to change the value of y to the name of the column in your input data that contains the adjusted p-values, for example:

...
y = 'padj',
...

Kevin

[MaxF]

Hi Kevin,

The enhancedVolcano package is awesome, thanks for making it.

Is there a reason you use unadjusted pvalue in the vignette? I am working with some data and was trying to weigh the pros and cons of visualizing with adjusted vs unadjusted p values.

[Kevin Blighe]

Hey, thanks for the comment. There is no rule about which to use, but, un-adjusted p-values are used more, based on my experience. Put it this way: I could not possibly see your work being rejected if you chose to use adjusted p-values

[Samantha]

Hi Kevin,

Jumping on this post after not finding any similar questions. If I set my y to "padj", can I still use pCutoff? Is pCutoff exclusive to p-values?

Thanks!

[Kevin Blighe]

Hello and good evening,

If you use 'padj', then pCutoff will also relate to adjusted pvalues. pCutoff will relate to whatever values you supply as the y-axis, basically.

Kevin