Hi  Im following RNAseq workflow for differential gene expression

Im using R command line. 

library(gplots)

library(RColorBrewer)

sampleDists<- dist(t(assay(rld)))

sampleDistsMatrix<- as.matrix(sampleDists)

xnames<- paste(colData(ddsFull)$SampleName,colData(ddsFull)$Sex,colData(ddsFull)$treatment)

dimnames(sampleDistsMatrix)<- list(xnames,xnames)

colors<- colorRampPalette(rev(brewer.pal(9,"Blues")))(255)

heatmap.2(sampleDistsMatrix,trace="none",col=colors,margins=c(10,10))

That seems like some error coming from heatmap.2, so I'm not sure about debugging. 

We are moving toward recommending the pheatmap package instead. Can you try this code from the workflow (search the page for "Sample distances")

http://www.bioconductor.org/help/workflows/rnaseqGene/