The inspect_raw_data() function won't plot data points where raw_data$concentration == NA, which is a problem because calculation of the donor bleed through (in correct_fret_signal()) relies on such data points.
On the other hand, setting raw_data$concentration == 0 for these points is easy to do when preparing the data file, but unpractical to handle properly in the code...
I encountered a case where obvious outliers existed in these data points (including a point where detection saturated), and they were not detected by inspection of the control plots (because not plotted).
These points were used to calculate the donor bleed through (Xd), which ultimately gave a Kd = 26.72 +/- 9.98.
Excluding them in the downstream analysis did not change the Kd significantly, giving Kd = 26.86 +/- 10.04.
In some cases, depending on the values of the "good" points and outliers, keeping outliers might significantly alter Kd (?).
Anyway, it would be good to offer a possibility to spot outliers even outside of the titration series, so the user has an opportunity to exclude these points if they decide so.
Not really a bug, more of a design problem.
The
inspect_raw_data()function won't plot data points whereraw_data$concentration == NA, which is a problem because calculation of the donor bleed through (incorrect_fret_signal()) relies on such data points. On the other hand, settingraw_data$concentration == 0for these points is easy to do when preparing the data file, but unpractical to handle properly in the code...I encountered a case where obvious outliers existed in these data points (including a point where detection saturated), and they were not detected by inspection of the control plots (because not plotted). These points were used to calculate the donor bleed through (Xd), which ultimately gave a Kd = 26.72 +/- 9.98. Excluding them in the downstream analysis did not change the Kd significantly, giving Kd = 26.86 +/- 10.04.
In some cases, depending on the values of the "good" points and outliers, keeping outliers might significantly alter Kd (?).
Anyway, it would be good to offer a possibility to spot outliers even outside of the titration series, so the user has an opportunity to exclude these points if they decide so.