Identical Z-Scores for Unregulated and Down-Regulated Genes Across Groups

[echovv]

Hey juju, thanks for your cool tools for great visualisation. I’ve encountered a somewhat strange issue: the Z-scores for all unregulated and down-regulated genes in the activated and control groups are identical (as shown in the left figure). However, when I examine the individual samples within the activated and control groups, I still observe differences in the Z-scores for each gene.

Could this be an issue related to how the Z-scores are being calculated? How can I address this to ensure the gene expression values looks like more reliable?

[junjunlab]

If the sample size is less than 3, for example, if you only have two samples, calculating Z-scores will result in the same value for each gene. It is recommended to provide at least three samples or more to calculate Z-scores.