I may ask how to plot EnhancedVolcano using padj instated of P-value?
What did you try already ?
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',
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.
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
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?
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.
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