Question: Heatmap with normalised count from DESEQ2
gravatar for ZheFrench
2.0 years ago by
ZheFrench300 wrote:

I was wondering which is better (or if one of this method is wrong ) for plotting in a heatmap normalised count from deseq2 : counts(dds,normalized=TRUE) : z-score( log2(norm count +1) ), z-score(norm count ) or just log2(norm count +1)

heatmap deseq2 • 2.9k views
ADD COMMENTlink modified 2.0 years ago by Kristin Muench520 • written 2.0 years ago by ZheFrench300

Take a look at how they are used in the DESeq2 vignette: Heatmap of the count matrix.

Normalised [unlogged; untransformed] counts are used for QC purposes and are neither logged nor Z-scaled. In addition, the default passed to pheatmap is scale="none".

For downstream analyses, you should really be using the regularised log or variance stabilised counts, and you can Z-scale these, if you wish. You do not have to log these.

Elsewhere, from EdgeR, people use logged CPM-normalised counts for heatmaps. For other tools that derive values in FPKM, people usually log those too (they can also be Z-scaled via the zFPKM function). You'll never see me use FPKM data, though.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Kevin Blighe65k
gravatar for Kristin Muench
2.0 years ago by
United States
Kristin Muench520 wrote:

I've used scale() with scale=TRUE, center=TRUE on rlog-normalized, which is a bit like z-score. I've seen people also plot log-scaled expression values too.

One tip - if you use asinh() instead of log2(), you can create the same kind of scaling, but you don't have to add 1 in order to account for possible cells that equal 0. For comparison:

enter image description here

enter image description here

ADD COMMENTlink written 2.0 years ago by Kristin Muench520
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1747 users visited in the last hour