Thanks ! I read the that but I have this situation:
topVarGenes <- order(-rowVars(assay(rld)))[0:1000]
mat <- assay(rld)[ topVarGenes, ]
mat<- mat - rowMeans(mat)
colnames(mat) <- paste0(metadata$CONDITION,"-",metadata$ID)
pheatmap(mat,method="complete",main = "Unsupervise 1000 genes ", show_rownames = F, color=color1,annotation_legend = TRUE, legend=T, cluster_cols=TRUE,file=nome)
If I use scale none or scale row I have a radical change of the cluster of my groups :
Here you have the images: http://imgur.com/a/uxxx8 The first one is the use scale=none e scale row. In the first case seem I have all my data is down-regulate...