Is the heatmap matruix from vst expressed in fold change?

Question

[Lila M]

Hi everybody, following the next code

vsd <- varianceStabilizingTransformation(dds, blind = TRUE)
vst <- assay(vsd)
dds2 <- DESeq(dds)
res2 <- results(dds2)
mat <- assay(vsd)[head(order(res.05$padj), 300), ]
write.table(mat, "heatmap_matrix")

I was wondering if in the final matrix (heatmap_matrix) the values are fold change or counts. Does anyone know about it?

Many many thanks!

Answer 1

[Devon Ryan]

I guess you could call the units "transformed counts" if you need to assign a name to things.

[Lila M]

Many thanks Devon for this information! !