Hi there,
I was wondering if you can help me understand the expression data in the developmental transcriptome of the Developing Human Brain atlas.
What is the difference between expression - log2 RPKM: 1 and expression - log2 RPKM: 2, for example? Is this a 2 fold difference?
Also, is this -log2, meaning the lower expression number actually has a higher expression in that region, or is it the higher the number, the higher the expression?
Many thanks!
Hi @ejw. Log2 normalized data means that a change in value of one (like your example going from 1 to 2) means a two-fold increase. This is true whether the values are positive or negative (e.g., changing from 1 to 2 and changing from -4 to -3 both result in a two-fold increase). If values are negative, it just means that RPKM is between 0 and 1 (nothing can be below 0 as you can’t have fewer than 0 fragments). There are a few other posts about, heatmap expression values, data normalization, and z-scores in other atlases that you may find useful.