I need to transform the score of a variable to z-scores, because of two different scales that were used according to the subjects' age. However, there are two groups: control and diseased. Do I compare the variable score to the mean and standard deviation of the control group i.e. z-score = (score - control mean)/SD in control group for each scale?
It depends on what your purpose is. If you want to compare individuals with different scores within the same treatment group, you would use the mean and standard deviation of the treatment group they're in. If you want to compare the average score between treatment groups, you would use the overall mean and standard deviation. If you standardized within each group, the mean difference would be exactly equal to 0 (i.e., because the means of the Z-score within each group would be equal to 0). To retain the differences between the treatment groups, the Z-scores should be computed with respect to the whole sample.