Threshold lines in EnhancedVolcano package

Question

[sato]

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.

https://github.com/kevinblighe/EnhancedVolcano#highlighting-key-variables-via-custom-point-sizes

My understanding is wrong? Please give me any advice to solve these problems.

Answer 1

[Kevin Blighe]

Is it possible for you to share the output that you are seeing?

With pCutoff set to 10e-3, the cut-off line will be drawn at 2 on the y-axis due to the fact that -log10(10e-3) == 2.