Question: deseq 2x2: highly variable genes are not among differentially expressed gene
gravatar for rahel14350
2.5 years ago by
United States
rahel1435010 wrote:


I did deseq 2x2 model. When I do a pheatmap for highly variable genes (using rld) the outcome are the genes that they are not even among the differentially expressed genes.

Here is my command for pheatmap:

topVarGenes <- head(order(rowVars(assay(rld)),decreasing=TRUE),20)
mat <- assay(rld)[ topVarGenes, ]
mat <- mat - rowMeans(mat)
df <-[,c("group","condition")])
pheatmap(mat, annotation_col=df)

For example for the gene with highest rld over samples, the basemean in dds is 98000 but the pvalue and padj is NA.

Can anyone help me with this issue? 

Many thanks in advance,


ADD COMMENTlink modified 4 months ago by Michael Love16k • written 2.5 years ago by rahel1435010
gravatar for Michael Love
2.5 years ago by
Michael Love16k
United States
Michael Love16k wrote:

topVarGenes looks at the row variance of the transformed values regardless of which samples come from which group. Differential expression testing asks whether the difference across group is large relative to the within-group variance. So these are different ways of ranking genes.

ADD COMMENTlink written 2.5 years ago by Michael Love16k
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