Table 1 YODA export output options.
Grouping Options: | Â |
|---|---|
none | Outputs info for each well or well position. |
average groups | Outputs average value and standard deviation for each well group described in well info. |
median groups | Outputs median value and standard deviation for each well group described in well info. |
Curve Parameter Options: | Â |
OD thresholds | The min and max background normalized OD values to use in doubling time calculation. |
Doubling time Interval OD | The min and max background normalized OD values to calculate "doubling time interval". The program will calculate the average doubling time over this interval. |
Survival time shift OD | The background normalized OD value to calculate time shift between curves at different age points. |
Run Export Options: | Â |
append ODs | Whether or not the OD readings for a well should be appended to output. |
subtract background | Outputs the OD readings with the file's background subtracted |
doubling time inflection | Outputs the doubling time calculated where the curve has the steepest slope between min and max OD thresholds. |
doubling time interval | Outputs the average doubling time calculated at all points between min and max doubling time threshold ODs. |
doubling time correction | Outputs empirically corrected doubling times. |
Lineage Export Options: | Â |
survival | Outputs the survival fractions for each age point. |
survival area | Outputs the integral of the survival fractions over all age points. |
clean | Survival fractions are cleaned so that the survival curve has no increases or gasping (spikes at end). |
show time shifts | Outputs the time shift relative to reference curve (first age point). |
doubling time method | The doubling time method used to calculate survival fraction (uses doubling time of first age point curve). |
% change versus reference | Calculates the percent change in survival integral of each well versus a reference. |
log2 ratio versus reference | Calculates the log base 2 ratio of survival integrals of each well versus a reference. |
t-test versus reference | Calculates the t-statistic and p-value for each well group versus a reference (grouping option must be selected). |