Hello all, I was trying to make a volcano plot with some real data, using log2(ratio) vs. Z-value significance. However the scatter of the points is too less contrary to 'normal' volcano plots and I'm getting a sharp 'V' shaped plot.
I understand that scatter occurs if one has different Y values for the Same X values. But what I'm missing here? The plot looks strange:(http://img402.imageshack.us/i/volcanoi.jpg/) The data(ratio) is available from pastebin or the file attached: http://pastebin.com/m2Jss3qF *The R Code:Am I doing something wrong here?* data <- read.table("data.txt",header=FALSE) ratio <- data$V1 ratio.mean <- mean(ratio) ratio.sd <- sd(ratio) ratio.log <- log2(ratio) z <- (ratio-ratio.mean)/(ratio.sd) z.sig <- 2*pnorm(-abs(z)) z.tsig <- 2*pt(-abs(z),df=length(ratio)-1)#sig from t-dist par(mfrow=c(1,4)) plot(ratio.log,-log10(z.sig)) plot(ratio.log, -log10(z.tsig)) plot(ratio.log,z.sig) plot(ratio,z) -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
