Because the few datasets I analyzed so far gave negative FRET values after correction by correct_fret_signal(), I added the following line to shift the entire curve upwards such that the minimal value becomes 0:
fret_corr <- fret_corr + abs(min(fret_corr))
This is a problem, because in case the function encounters a dataset that, for some reason, doesn't give negative values, the curve will be shifted up regardless, whereas this is not necessary in this case. This operation can be bypassed easily by checking the occurrence of negative values before.
In case there is no negative value, should the curve be shifted down such that the lowest value becomes zero?
This is not critical, because the absolute vertical position of the curve does not influence the determination of Kd, but the bigger question is: how to give the user an accurate idea of the background before a vertically shifted curve is produced? Maybe in a step before correction?
Because the few datasets I analyzed so far gave negative FRET values after correction by
correct_fret_signal(), I added the following line to shift the entire curve upwards such that the minimal value becomes 0:This is a problem, because in case the function encounters a dataset that, for some reason, doesn't give negative values, the curve will be shifted up regardless, whereas this is not necessary in this case. This operation can be bypassed easily by checking the occurrence of negative values before.
In case there is no negative value, should the curve be shifted down such that the lowest value becomes zero?
This is not critical, because the absolute vertical position of the curve does not influence the determination of Kd, but the bigger question is: how to give the user an accurate idea of the background before a vertically shifted curve is produced? Maybe in a step before correction?