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...ut getting separate colors for anything above 4.5 and less than -4.5? plot(three, type="h", col=ifelse(three > 4.5, "red", "black"), xlim=c(0,500), ylim=range(three), lwd=2, xlab="Chromosome", ylab="Z-Score", font.lab=2, font=2, main="Upregulated Genes in Patient Sample") Thanks in advance, Patrick The information transmitted is intended only for the per...{{dropped:10}}

Dear All, I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams. The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2. I am