Question: Is the heatmap matruix from vst expressed in fold change?
0
gravatar for Lila M
21 months ago by
Lila M 470
UK
Lila M 470 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 21 months ago by Devon Ryan89k • written 21 months ago by Lila M 470
2
gravatar for Devon Ryan
21 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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

ADD COMMENTlink written 21 months ago by Devon Ryan89k

Many thanks Devon for this information! !

ADD REPLYlink written 21 months ago by Lila M 470
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