Hi all, Thanks to Dan, I now know how to get genes highlighted in a Volcano plot based on p-values from the results of my limma analysis. I would like to get a list of the genes highlighted. For example, the code below gives me a volcano plot with the top 10% genes based on p-values highlighted. windows() pdf("VolcanoPlot_GSExxxxxx_10perc.pdf"); results$threshold = as.factor(results$P.Value<=quantile(results$P.Value, 0.1)) g = ggplot(data=results, aes(x=logFC, y=-log10(P.Value), colour=threshold)) + geom_point(alpha=0.4, size=1.75) + opts(legend.position = "none") + xlim(c(-5, 5)) + ylim(c(0, 8)) + xlab("log2 fold change") + ylab("-log10 p-value") g dev.off() This code below gives me the exact 10% threshold value: results = topTable(fit2, adjust ="BH", number = nrow(gse25724dat[[1]]), sort.by="P") results2 = quantile(results$P.Value, 0.1) What I would like however is a list/table of the genes that meet this criteria, i.e, the genes highlighted from the first code. Any help will be greatly appreciated. Thanks. -Avoks

On Wed, May 9, 2012 at 8:21 AM, Ovokeraye Achinike-Oduaran < ovokeraye@gmail.com> wrote: > Hi all, > > Thanks to Dan, I now know how to get genes highlighted in a Volcano > plot based on p-values from the results of my limma analysis. I would > like to get a list of the genes highlighted. For example, the code > below gives me a volcano plot with the top 10% genes based on p-values > highlighted. > > windows() > pdf("VolcanoPlot_GSExxxxxx_10perc.pdf"); > results$threshold = as.factor(results$P.Value<=quantile(results$P.Value, > 0.1)) > g = ggplot(data=results, aes(x=logFC, y=-log10(P.Value), > colour=threshold)) + > geom_point(alpha=0.4, size=1.75) + > opts(legend.position = "none") + > xlim(c(-5, 5)) + ylim(c(0, 8)) + > xlab("log2 fold change") + ylab("-log10 p-value") > g > dev.off() > > This code below gives me the exact 10% threshold value: > > results = topTable(fit2, adjust ="BH", number = > nrow(gse25724dat[[1]]), sort.by="P") > results2 = quantile(results$P.Value, 0.1) > > What I would like however is a list/table of the genes that meet this > criteria, i.e, the genes highlighted from the first code. Any help > will be greatly appreciated. > > top10pct = results[results$P.Value<=results2,] As an aside, I noticed that you are working with unadjusted p-values. I would not recommend doing so and would suggest using an adjusted p-value instead in most cases. Sean [[alternative HTML version deleted]]

Thanks Sean. Duly noted. I understand that the unadjusted p-values are not corrected for multiple testing. But thanks a bunch. -Avoks On Wed, May 9, 2012 at 2:21 PM, Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com=""> wrote: > Hi all, > > Thanks to Dan, I now know how to get genes highlighted in a Volcano > plot based on p-values from the results of my limma analysis. I would > like to get a list of the genes highlighted. For example, the code > below gives me a volcano plot with the top 10% genes based on p-values > highlighted. > > windows() > pdf("VolcanoPlot_GSExxxxxx_10perc.pdf"); > results$threshold = as.factor(results$P.Value<=quantile(results$P.Value, 0.1)) > g = ggplot(data=results, aes(x=logFC, y=-log10(P.Value), colour=threshold)) + > ?geom_point(alpha=0.4, size=1.75) + > ?opts(legend.position = "none") + > ?xlim(c(-5, 5)) + ylim(c(0, 8)) + > ?xlab("log2 fold change") + ylab("-log10 p-value") > g > dev.off() > > This code below gives me the exact 10% threshold value: > > results = topTable(fit2, adjust ="BH", number = > nrow(gse25724dat[[1]]), sort.by="P") > results2 = quantile(results$P.Value, 0.1) > > What I would like however is a list/table of the genes that meet this > criteria, i.e, the genes highlighted from the first code. Any help > will be greatly appreciated. > > Thanks. > > -Avoks