[BioC] DeSeq Volcano plot- error
Wolfgang Huber
whuber at embl.de
Wed Mar 21 22:38:05 CET 2012
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
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