I want to create a supervised heatmap for the differential expression data obtained from rnaseq analysis using deseq2.
I'm not able to see the up and down genes cluster expression even if I plot only differential expresion data results.
dds <- DESeq(dds) res<-results(dds) resOrdered <- res[order(res$padj),] head(resOrdered) select_genes<-rownames(subset(resOrdered, padj < 0.1)) pheatmap(assay(rld)[ select_genes,],cluster_rows =F) heatmap.2(assay(rld)[ select_genes,] ,density.info = "none",symm=F,Colv =T,trace="none")
If I want to sho better the upregolted gene and downregulate what can I do?
thanks so much!