Endy:Victor3 plate reader/Measurement variation

Fluorescence
I measured the fluorescence of a well containing E. coli expressing YFP and a well containing untransformed MG1655. Ten measurements were taken over a 5min period.

Absorbance
I measured the absorbance of the same wells. Measurements were taken over the same 5min period.

Correlation in noise between adjacent wells
The absorbance of three adjacent wells was measured over 20 hours at 37C with shaking. The wells contained BL21(DE3) growing in Neidhardt EZ Rich Defined.

Figure 1 on the right shows the rate of change of absorbance over time. The variation in these rates are clearly highly correlated and this is expected to be due to machine variation rather than variations in the absorbance of the bacterial culture. The correlation between each of these time series is >.775 which is highly significant (p-value <10E-16). This data suggests that averaging replicate cultures in adjacent wells may not remove the kind of machine variation seen here. Fitting a line to the data or smoothing the data may be necessary. The correlation between these time series and a media blank located elsewhere on the plate was less than between the replicates but still significant (correlation ~0.4, p-value = 0.0001). This suggests that some but not all of the machine variation seen in Figure 1. can be removed by subtracting a media background.