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

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

rna-seq • 2.7k views
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What did you try already ?

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3.0 years ago

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:

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Kevin

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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.

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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

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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!

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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