Box plot of gene expression data

Question

[a.stef.44]

Hello,

I would like to visualize gene expression of significant genes between case/control, but I am not sure which values to use. Count data, vst normalized counts data, or DESeq2 normalized data?

Thank you in advance, Aleksandra

[ATpoint]

It doesn't matter as long as it is normalized to account for differential sequencing depth and library composition. If you have vst then use this, it's usually a good choice. Don't show raw counts, the rest is ok.