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.
*Am I doing something wrong here?* The data(ratio) is available from pastebin: http://pastebin.com/m2Jss3qF 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) [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
