[BioC] DeSeq Volcano plot- error

[Wolfgang Huber]

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
>
>
>
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber