"Enhanced Volcano" package - how to set p adjusted cut off?

Question

[tanya_fiskur]

Hello everyone!

There is a nice package, Enchanced Volcano, for plotting differential expression analysis results. There is a way to set pCutoff and FCcutoff. Is it possible to set p adjusted cutoff?

Thank you!

[rhizorick]

I found a pretty easy workaround. I just created a new data frame and replaced the p-values with the adjusted p-values. It worked. You just need to be cognizant of the fact that your new data frame is basically "mislabeled" if you wish to share the raw data. So I recommend keeping your original data frame and using the modified data frame only for visualization.

[Kevin Blighe]

Thank you

Answer 1

[Kevin Blighe]

Hey, if you use adjusted p-values (q-values), then, for example, a pCutoff of 0.05 just relates to FDR q = 0.05.

Volcano plots are typically drawn from nominal p-values, though

Kevin

[Mozart]

Kevin, sorry for resurrecting this old post. Not sure I have got this right. In the default settings, the parameter pCutoff stands for nominal p value, right? what if one wants to use p adjusted ones, instead?

Sorry for my naive question but, why in a volcano plot nominal p values are preferred over adjusted ones? thanks in advance

[Kevin Blighe]

Hey Mozart, there is no 'written rule' on this topic. When you perform FDR adjustment, many p-values may be converted to a value of 1.0, or some other constant value. So, the argument to use nominal p-values may purely be about the aesthetics of the final plot.

[Mozart]

thanks a lot for that!