Question: Is the heatmap matruix from vst expressed in fold change?
0
gravatar for Lila M
2.6 years ago by
Lila M 800
UK
Lila M 800 wrote:

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!

ADD COMMENTlink modified 2.6 years ago by Devon Ryan93k • written 2.6 years ago by Lila M 800
2
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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

ADD COMMENTlink written 2.6 years ago by Devon Ryan93k

Many thanks Devon for this information! !

ADD REPLYlink written 2.6 years ago by Lila M 800
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