[BioC] DeSeq Volcano plot- error

[Melissa.Martin at lshtm.ac.uk]

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