I am doing two RNA-seq analysis with unequal sample size both. In the first one, I use 10 healthy controls and 52 patients and I obtain good results when I use logFC=|2| y p-adj 0.01. Nevertheless, when I analyze the population of 7 healthy controls and 58 patients I obtain this volcano plot, which looks really strange. I have never had problems plotting it, so I think that the code I am using is correct. What might be the problem?
alpha <- 0.01
cols <- densCols(res$log2FoldChange, -log10(res$pvalue))
plot(res$log2FoldChange, -log10(res$padj), col=cols, panel.first=grid(),
main="Volcano plot", xlab="Effect size: log2(fold-change)", ylab="-log10(adjusted p-value)",pch=20, cex=0.6)
gn.selected <- abs(res$log2FoldChange) > 2 & res$padj < alpha
lab=rownames(res)[gn.selected ], cex=0.4)
Thanks so much,