data frame from deseq2

Question

[1769mkc]

I m plotting heatmap, based on padj value this is the code im using .

padj <- 0.05
res.index <- which(res$padj < padj)
df <- as.data.frame(
  colData(dds[res.index,])[,c("condition")])
rownames(df) <- colnames(assay(rld[res.index,]))

library(pheatmap)
pheatmap(assay(rld[res.index,]),
         cluster_rows=TRUE,
         show_rownames=FALSE, cluster_cols=TRUE,
         treeheight_col=1,
         scale="row",
         annotation_col=df)

Im getting the heatmap no issues but i want to get the value which im using for my plot , how i get that, any suggestion or help would be highly appreciated .

[VHahaut]

Do you mean the rld normalized count table?

assay(rld[res.index,]

[1769mkc]

yes..how do i get that?

Answer 1

[VHahaut]

Ok so you mean you want to save it as a text file somewhere?

write.table(assay(rld[res.index,]), sep="\t", path, row.names=F, quote=F)

where path should be replaced by the full path where you want to save it such as:

    write.table(assay(rld[res.index,]), sep="\t", "~/Desktop/rld_normalized_count.txt", row.names=F, quote=F)

[1769mkc]

thanks a lot...i was looking to get the data so that i can use it for other analysis