What is the Z score reference value in RNAseq GBM data?

Hi @SB5. I would suggest starting with this community forum post about normalization and Z-scores. You are not the first to have questions about this data set (see this post). In general, the expression values are normalized, within-sample gene expression measures that are log-normalized so the data across samples approximates a normal distribution. Z-scores are then defined as usual (x-mean(x))/sd(x). Z scoring is done irrespective of sample meta-data, and any differential expression analyses are comparing whatever is selected in the source vs. target groups.