Due to poor quality of precast gels for second dimension we chose to use lab-made gels. Despite the same degree of cross-linking of the both there a severe differences in spot patterns, such as a proper spot matching is virtually not possible. On the other hand, the gels within the groups are consistent. Did you notice similar problems and how did you solve them- without repeating the gels (which is no option because of no material left for any further processing).
Thank you for your help.