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.