I've been struggling to draw a volcano plot by EnhancedVolcano package.
I want to set a threshold of p-value at 0.05 (-log10P=1.3) but 'pCutoff = 1.3' doesn't show the horizontal threshold line. And besides, 'pCutoff = 10e-3' ( p= 0.001, -log10P=3) shows a incorrect horizontal line. The line is slightly lower than the correct line based on the labels in the longitudinal axis.
Here is the code I used.
EnhancedVolcano(data.frame(myfilename), lab = rownames(myfilename), x = 'log2FC', y = 'pvalue', xlim = c(-1.5, 1.5), title = 'Title', pCutoff = 10e-3, FCcutoff = 0.58 )
In a tutorial page below ('Highlighting key variables via custom point sizes' section), I noticed that 'pCutoff = 10e-4' creates a hrozontalline line at -log10P=3.
My understanding is wrong? Please give me any advice to solve these problems.