Question: Creating a heatmap from DGE data
gravatar for freakyfliss1
6 months ago by
freakyfliss10 wrote:

Hi there, Apologies if this question is a repeat, but I couldn't find the answer I'm looking for on here or youtube. Perhaps someone could point me in the right direction?

I have the DGE RNA-seq data for a gene knock down experiment versus a control (with 3 repeats and 3 control repeats). I have 718 genes and have the log2 fold change (LFC) for all of the genes.

In my .txt file that I read into R: I have gene names in the row, and LFC in a single column. Can I plot a heatmap from this data? I want to be able to visualise which genes are up-regulated or down-regulated and how they cluster. All the other heatmap tutorials I have seen have plotted data for 2 or more columns.

I am unsure how to proceed now I have read this file in.

Best wishes!

heatmap • 279 views
ADD COMMENTlink written 6 months ago by freakyfliss10

Prior answer from @Kevin: A: How can I generate Heat Map with dendograms, and PCA analysis in "R Programming"

ADD REPLYlink written 6 months ago by genomax80k

Also see this collection of tutorials: Heatmaps in R

ADD REPLYlink written 6 months ago by ATpoint31k
  1. You can plot heatmap with 1 column. But you may need some knowledge of writing the script to customize you heatmap.
  2. It doesn't make sense to me to cluster with just 1 column. Isn't it just a sorting?
ADD REPLYlink written 6 months ago by shoujun.gu290

Right! I am struggling to find a guide that will help me with the code for this. I keep getting an error in R saying I need more than one column.

ADD REPLYlink written 6 months ago by freakyfliss10

Instead of plotting the average LFC you could plot the read counts in each replicate and each treatment status (total 6) and then plot that heat map. You can do this only for De genes and see how they cluster.

ADD REPLYlink written 6 months ago by Fabio Marroni2.5k
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