Question: data frame from deseq2
0
gravatar for krushnach80
11 weeks ago by
krushnach80200
krushnach80200 wrote:

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 .

rna-seq R • 201 views
ADD COMMENTlink written 11 weeks ago by krushnach80200
1

Do you mean the rld normalized count table?

assay(rld[res.index,]
ADD REPLYlink written 11 weeks ago by VHahaut1.0k

yes..how do i get that?

ADD REPLYlink written 11 weeks ago by krushnach80200
1
gravatar for VHahaut
11 weeks ago by
VHahaut1.0k
Belgium
VHahaut1.0k wrote:

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)
ADD COMMENTlink written 11 weeks ago by VHahaut1.0k

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

ADD REPLYlink written 11 weeks ago by krushnach80200
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1491 users visited in the last hour