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!
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tanya_fiskur •
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
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
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.
Yes, I saw it, but it's not adjusted p value. It would be too strict, if 10e-6 was a usual FDR :)
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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.
Thank you