Question: Deseq2 unsupervised analysis (heatmap row scaling or none?)
0
gravatar for jarod_v6@libero.it
3.5 years ago by
Italy
jarod_v6@libero.it40 wrote:

I would like to do a unsupervised heatmap using deseq2 counts.

If I use :

 

topVarGenes <- order(rowVars(assay(rld)),decreasing=TRUE)[1:1000]
mat <- assay(rld)[ topVarGenes, ]
mat <- mat - rowMeans(mat)
pheatmap(mat, annotation_col=df)

 

Which is the right way to do? Using scale="row" or scale="none"?

 

 

deseq2 pheatmap • 1.8k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by jarod_v6@libero.it40

What do you mean by 'right way'?

ADD REPLYlink written 3.5 years ago by b.nota330

I mean what is the way to perform the unsupervised analysis starting from DeSeq2 package.

ADD REPLYlink written 3.5 years ago by jarod_v6@libero.it40
Answer: Deseq2 unsupervised analysis
3
gravatar for Michael Love
3.5 years ago by
Michael Love24k
United States
Michael Love24k wrote:

We recommend scale="none" in the workflow.

Here is a previous post where I give some rationale for this decision:

A: Biclustering Normalizing by Row in Heatmap of DESeq2

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Michael Love24k
Answer: Deseq2 unsupervised analysis (heatmap row scaling or none?)
0
gravatar for jarod_v6@libero.it
3.5 years ago by
Italy
jarod_v6@libero.it40 wrote:

Thanks ! I read the that but I have this situation:

topVarGenes <- order(-rowVars(assay(rld)))[0:1000]

 

mat <- assay(rld)[ topVarGenes, ]
mat<- mat - rowMeans(mat)
colnames(mat) <- paste0(metadata$CONDITION,"-",metadata$ID)

#draw heatmap
nome<- "Image_analisi/Unsupervised_1000highvariation.png"
pheatmap(mat,method="complete",main = "Unsupervise 1000 genes ", show_rownames = F, color=color1,annotation_legend = TRUE, legend=T, cluster_cols=TRUE,file=nome)

 

If I use scale none or scale row  I have a radical change of the cluster of my groups :

Here you have the images: http://imgur.com/a/uxxx8 The first one is the use scale=none e scale row. In the first case seem I have all my data is down-regulate...

 

 

ADD COMMENTlink written 3.5 years ago by jarod_v6@libero.it40
1
The color mapping is not good here for two reasons: 1/12 men are color blind and red/green is very difficult to distinguish The 0 value is not set to black If you have more questions on pheatmap or plotting but not related to DESeq2 functions feel free to post them as new questions but without the DESeq2 tag.
ADD REPLYlink written 3.5 years ago by Michael Love24k
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