Hello, I am writing with a question about edgeR function smearPlot. I made a smear plot but am seeing rows of orange points below and above (-5,-5) and (5,5) respectively. Here are the commands I used to make the plot: n.shoot = sum(summary(decideTestsDGE(et.shoot,p.value=0.05))[c(1,3),]) plotSmear(et.root,de.tags=rownames(topTags(et.root,n=n.root)$table),ma in="Root") abline(h = c(-2, 2), col = "dodgerblue") In case the attachment doesn't go through I put the plot on-line (temporarily) at http://vm142-20.iplantcollaborative.org/pl.png/ Best wishes, Ann -------------- next part -------------- A non-text attachment was scrubbed... Name: pl.png Type: image/png Size: 79161 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20120828="" 8d3a973c="" attachment.png="">