Question: plotting an expression data in heat map/ hierarchical clustering
0
gravatar for rob.costa1234
13 months ago by
rob.costa1234160
United States
rob.costa1234160 wrote:

I have an RNAseq data expression matrix 200 rows and 12 columns. I want to show as gradient in expression profiles using either HC or simple heat map. The experiment is to show that with treatment certain genes are upregulated as compared to vector vs expressed gene, while with mutant this expression for same subset of genes goes down. What will be my best option. I dont want to show by line graph.

Thanks kanwar

rna-seq • 515 views
ADD COMMENTlink written 13 months ago by rob.costa1234160
1

ComplexHeatmap

ADD REPLYlink written 13 months ago by venu6.1k

I feel like heatmap would be better as clustering methods would not give any idea of up/downregulation, and also you can cluster your samples while plotting the heatmap.

ADD REPLYlink written 13 months ago by firatuyulur260
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