Create Volcano Plot

General
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3

It is difficult to answer without a reproducible example however this should make your volcano plot:

library (ggplot2)
EM <- read.csv(file = "D:/metabolomics/4E5/em.csv", row.names = 1)

df <- data.frame(log10FC = log10(EM$Fold.changes),
                 logpv = -log2(EM$pvalues))

ggplot(df, aes(x=log10FC, y=logpv)) +
  geom_point()

Maybe it would help working through the NormalizeMets vignette which guides you through an example analysis.