I am having trouble with the normalization of internal reference positions. After selecting Normalization > Update Normalization, the bands do not move and the arrows remain. Why do the internal reference positions not normalize?
You have to be careful when using internal reference positions, especially when you also have defined external reference positions. The program will always grant priority to the external reference positions, because these bands are the most important: they normalize the gel to become compatible with other gels.
Therefore, when a close external reference position says to a lane position “Move down”, while an internal reference position says “Move up”, this lane will finally move down, to respect the compatibility with the reference system. The further a position occurs from any reference position (in all directions), the more freedom it has to be adjusted according to an internal reference position. This explains why some positions are not updated as you would expect it to happen.