Choose between pvalue & pvalue.adj

Question

[Guitout]

Hi everyone,

I am currently carrying out a DE analysis on single cell, I have just arrived at the volcano plot and I do not know what to use for the y axis: the pval or the pval.adj.

From what I understood, the pval.adj are calculated because of the multiple test problem, but I would like to know whether to use the pval.adj every time or only if the histogram of the pval is not good (or other reason).

Thank you in advance for your help.

Answer 1

[Istvan Albert]

You should use the correct p-value depending on what you are trying to test for.

If the effect size you are testing for can be affected by multiple comparisons then you should use .adj. If the effect size that you are testing for is not affected by multiple comparisons then you should use the unadjusted p-value.