Heatmap from count matrix

Question

[Confused_human]

Hi everyone,

I have a feature count matrix which looks like this

GeneID  sample 1    sample 2    sample 3
gene1   0   1   7
gene2   120 6   0
gene3   0   100 8

I want to create a heatmap of this data where I want to show the differentially expressed genes to know up regulated and down regulated genes which are differentially expressed.

I tried it with R. But I'm not getting the heatmap. Is there any way to generate heatmap from the count matrix table?

[rpolicastro]

Both the edgeR and DESeq2 manuals go through the steps to make this type of figure. What problem(s) are you running into more specifically? If you provide us specific errors or points of confusion we can help you work through it.

[Ram]

1. You have gene counts, not fold change for DE genes. Those are two different datasets.
2. You say you tried with R, but you don't show us what exactly you tried. Please show us the code.
3. "I'm not getting the heatmap" is like saying "it doesn't work". It says nothing about what exactly is happening. Be as descriptive as you can about the problem. We should be able to reproduce the error on our end if we try your code using your data on the versions of software you're using. Include ALL of that information.

Answer 1

[ATpoint]

Scaling RNA-Seq data before clustering?

Use the second heatmap code chunk, with the scaling.