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What are the values shown on DESEQ2 heatmap legend?

I have this heatmap which represents 4 conditions and 5 timepoints each. I understand that when I use z-score the legend refers to the standard deviations. However, when you're not using z-scores what do those values represent? It says 0 to 20, but of what? What would 20 be? 20 transcripts? 20,000 transcripts? 20 FPKM?

I have checked the vignette but I am not finding the answer to my question.

My organism has ~5.5k genes.

enter image description here

heatmap rna-seq deseq2 r pheatmap
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updated by karl.stamm karl.stamm • written by mgranada3 • mgranada3

Can you show us the code you're using to generate the heatmap? I don't think DESeq2 plots FPKM - it must be one of either raw counts or normalized counts.

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written by Ram Ram

My count matrix was made using featureCounts and I read this into DESeq2.

I don't know how much code you need but this is just the heatmap:

> library("pheatmap")
> df <- as.data.frame(colData(dds)[,c("condition","type")])
> select <- order(rowMeans(counts(dds,normalized=TRUE)), decreasing=TRUE)
> pheatmap(assay(vsd)[select,], cluster_rows=TRUE, show_rownames=FALSE,
     cluster_cols=FALSE, annotation_col=df)
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written by mgranada3 • mgranada3

Well you're clearly plotting assay(vsd) so what's that?

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written by karl.stamm karl.stamm

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