Question

Heatmap of selected genes

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danikadigiacomo • 0

@danikadigiacomo-21480

Last seen 5.4 years ago

Hi all! I analyzed my RNAseq data with DESeq2 and I obtained a nice unsupervised Heatmap with my top 20 or top 50 DEGs. Now I would create a Heatmap showing only a list of about 15 genes of interest. Is there a way to do it? Thank you, Danika

heatmap DEGs RNAseq DESeq2 • 4.5k views

ADD COMMENT • link updated 5.4 years ago by mikhael.manurung ▴ 280 • written 5.4 years ago by danikadigiacomo • 0

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Hi Danika,

I also need to do the same with a list of DEGs. Are you using FPKM values to plot the heatmap?

Thanks, Hamid

ADD REPLY • link 4.6 years ago Hamidreza Hashemi ▴ 20

score 0 · Answer 1 · 2019-07-29

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mikhael.manurung ▴ 280

@mikhaelmanurung-17423

Last seen 2.5 years ago

Netherlands

You can do this easily with pheatmap package from CRAN (or ComplexHeatmap if you want something from Bioconductor).

pheatmap(your_deg_matrix)

Dave Tang made a good tutorial on this.

ADD COMMENT • link 5.4 years ago mikhael.manurung ▴ 280