If the Z score formula still doesn’t work, it may be the difference between downloading the data at the level of samples vs. structures. Can you try following this steps from this post for downloading the data at the sample level and then calculating the Z scores to see if you get the expected answer? You are correct that “x” is the vector corresponding to expression levels for a given probe when calculating Z scores. If this still doesn’t solve your problem, or if you would prefer to use the API, please post again and I’ll see if I can find someone else to address the question.