Niormalization process in creating heatmap

Question

[ZuelTech]

Hi! I am creating heatmap to determine gene expression. In normalization procedures of the heatmap pipeline, is log2 transformation needed before performing Z-score normalization? Is this procedure standard for heatmap visualization?

Answer 1

[ATpoint]

I gave my standard here Scaling RNA-Seq data before clustering?

This has been asked many times before.

[ZuelTech]

In my case, I performed log2 transformation, then do Z-score normalization. Is that acceptable doing 2 normalizations to create a single heatmap?

[ATpoint]

Frankly, if you had read my link you would not be asking this. This is answered in the link, read it.

[ZuelTech]

Thank you! It's in the last line. So we do log2-transform the normalized read counts before Z-scaling!