Weird looking volcano plot

Question

[Harini]

Hello!

I am working with a plasma proteomics expression array and my volcano plot for DEA looks a bit atypical. Here is the code that I used (I am a novice coder, so please pardon any poor coding)

volplot1 <- ggplot(data = vol.redB, 
                  aes(x = AVG.Log.Ratio, y = -log10(Protein.Pvalue), 
                        col = diffexpressed, label = delabel)) + 
theme_light() + 
geom_vline(xintercept = c(-0.6, 0.6), col = "black", linetype = "dashed", linewidth = 0.1) + 
geom_hline(yintercept =-log10(0.05), col = "black", linetype = "dashed", linewidth = 0.1) + 
geom_point(size = 0.5) + 
geom_text_repel(size = 3.5, force = 3, max.overlaps = 10, point.size = 10, box.padding = 0.5) + 
scale_color_manual(values = c("#ff595e", "#5e6472", "#ff595e"), label= c("PRE", "", "POST")) + 
labs(
    title = "", 
    x = "log2(FC) - enrichment", 
    y = "-log10(adj.pvalue) - significance", 
    color = "")

This is the "atypical" volcano plot.

I suspect maybe this is because of some missing values in my dataset, although I could be wrong. Any ideas from others for a possible explanation and required fix? Many thanks in advance!

[yura.grabovska]

Can you explain what is atypical about the plot? Do you mean that the majority of the points are below threshold? Or something else?

[Juan]

Hi!

I think the most important thing is to explain the pre-processing process. Which normalisation method did you use? Was batch correction performed? How did you identify the DEA (which method)?

The volcano plot is just reflecting the results obtained from those previous steps.