log10 transformation (l1223 in Asko.R) returns Inf when p-value are 0. A possible solution might be to add 1e-314 to the pvalue (or .Machine$double.xmin) each time the og10(pvalue) is calculated :
with(tglm, plot(tglm$logFC, -log10(tglm$PValue + .Machine$double.xmin), pch=16, cex=0.5, xlim=c(min(tglm$logFC)-0.5, max(tglm$logFC)+0.5), ylim=c(min(-log10(tglm$PValue + .Machine$double.xmin))-0.5, max(-log10(tglm$PValue + .Machine$double.xmin))+0.5), main=paste0("Volcano plot - ", contrast), xlab="Log2FoldChange", ylab="-log10(pvalue)"))
log10 transformation (l1223 in Asko.R) returns Inf when p-value are 0. A possible solution might be to add 1e-314 to the pvalue (or .Machine$double.xmin) each time the og10(pvalue) is calculated :
with(tglm, plot(tglm$logFC, -log10(tglm$PValue + .Machine$double.xmin), pch=16, cex=0.5, xlim=c(min(tglm$logFC)-0.5, max(tglm$logFC)+0.5), ylim=c(min(-log10(tglm$PValue + .Machine$double.xmin))-0.5, max(-log10(tglm$PValue + .Machine$double.xmin))+0.5), main=paste0("Volcano plot - ", contrast), xlab="Log2FoldChange", ylab="-log10(pvalue)"))