The Open qPCR provides data on the fluorescence value, background subtracted value, and baseline subtracted value for each channel of each PCR well. These values are included in the amplification_data.csv file included in your individual experiment exports.
Fluorescence values are raw fluorescence measurements taken by the Open qPCR before taking calibration into account.
Background subtracted values take the calibrated values (post calibration for water, HEX, and FAM) into account to adjust for well-to-well variation. This is dependent on the data generated from the calibration that you perform. The values here have not gone through baseline subtraction.
Baseline subtracted values are the fluorescence values after the software performs baseline alignment of the amplification curves. Baseline refers to the background signal level prior to any significant product amplification. By turning baseline subtraction on, the software takes the baseline portion of each curve and brings it to 0. Baseline subtraction has no impact on Cq for the Cy0 and cpD2 methods.