Hello, I am trying to make a volcano plot using DeSeq to display my differentially expressed genes. I am working with RNAseq data from bacteria (wild-type vs knockout). I have followed the code that was supplied in the Suppliment II Material from "Differential expression analysis for sequence count data" but received this error: Error in eval(substitute(groups), data, environment(x)) : numeric 'envir' arg not of length one I have follwed the code almost exactly but defined log="x". Here is the code I have entered: print(xyplot( -log10( pval ) ~ log2FoldChange, + res$baseMean, + log="x", pch=20, cex=.2, + col=ifelse( res$padj<.1, "#FF000050", "#00000050" ), + axis = function( side, ... ) { + if( side=="bottom") { + panel.axis( side, outside=TRUE, at=seq(-14,14,by=1), labels=FALSE ) + panel.axis( side, outside=TRUE, at=seq(-10,10,by=5), labels=TRUE ) + } + if( side=="left") { + panel.axis( side, outside=TRUE, at=seq(0,25,by=1), labels=FALSE ) + panel.axis( side, outside=TRUE, at=seq(0,25,by=5), + labels = do.call( expression, + lapply( seq(0,25,by=5), function(a) + substitute( 10^-b, list(b=a) ) ) ) ) + }}, + xlab = "log2 fold change", ylab = "p value", + scales = list( + x = list( limits=c( -6, 6 ) ), + y = list( limits=c( 0, 25 ) ) ) )) Many Thanks! Melissa

Dear Melissa does the code work for you if you reproduce it exactly from the example? Once that is established, you could start making changes and then see when what breaks. Also, why do you want to set log="x"? The data that you are supplying for the x-axis, log2FoldChange, are already on the log-scale, so that argument does not seem necessary (in fact: wrong). Also, if the complexity of lattice of plots is overwhelming, you can always use the basic R plots: plot( log2FoldChange, -log10( pval ) ) Best wishes Wolfgang Mar/21/12 6:32 PM, Melissa.Martin at lshtm.ac.uk scripsit:: > Hello, > > I am trying to make a volcano plot using DeSeq to display my differentially expressed genes. I am working with RNAseq data from bacteria (wild-type vs knockout). > > I have followed the code that was supplied in the Suppliment II Material from "Differential expression analysis for sequence count data" but received this error: > > Error in eval(substitute(groups), data, environment(x)) : > numeric 'envir' arg not of length one > > I have follwed the code almost exactly but defined log="x". Here is the code I have entered: > > print(xyplot( -log10( pval ) ~ log2FoldChange, > + res$baseMean, > + log="x", pch=20, cex=.2, > + col=ifelse( res$padj<.1, "#FF000050", "#00000050" ), > + axis = function( side, ... ) { > + if( side=="bottom") { > + panel.axis( side, outside=TRUE, at=seq(-14,14,by=1), labels=FALSE ) > + panel.axis( side, outside=TRUE, at=seq(-10,10,by=5), labels=TRUE ) > + } > + if( side=="left") { > + panel.axis( side, outside=TRUE, at=seq(0,25,by=1), labels=FALSE ) > + panel.axis( side, outside=TRUE, at=seq(0,25,by=5), > + labels = do.call( expression, > + lapply( seq(0,25,by=5), function(a) > + substitute( 10^-b, list(b=a) ) ) ) ) > + }}, > + xlab = "log2 fold change", ylab = "p value", > + scales = list( > + x = list( limits=c( -6, 6 ) ), > + y = list( limits=c( 0, 25 ) ) ) )) > > > Many Thanks! > > Melissa > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber