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Noise is defined as the standard deviation of signal intensity of the liver divided by the average signal intensity of the liver within each ROI [11].
To normalize the mean signal intensities, they were divided by the average signal intensity in the monocular segment (200 pixels long by 40 pixels wide).
The reported signal strength is then the best average signal difference divided by the average signal.
Background was calculated for each array by the average signal of the negative control probes.
The staining intensity of each tissue section was assessed by the average signal intensity and the percentage of positive cells.
Data was normalized by dividing the difference between signal and background signal by the average signal for the respective fluorophore.
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To identify genes differentially expressed under the different treatments, the fold-changes were calculated by dividing the average signal of the treatment by the control, and genes with a fold-change greater or lesser than a given threshold were chosen.
The normalized ratio (R) was calculated by dividing the average signal from the Wt probe by the sum of the signals from the average Wt and average Mt probes (SWt/(SWt+SMt)) (Figure 1).
After detection, spots are fitted with a 3D Gaussian function and the GMM approach applied as detailed in Supplementary Note 2. In short, the algorithm reconstructs the mRNA foci in multiple single mRNA by using the average signal of a single mRNA as a reference.
The baseline was measured automatically by calculating the average signal of the whole sweep and subtracting it from the trace (ASA-vers. 4.6 by ANT software).
Baseline was measured automatically by calculating the average signal on the whole sweep and subtracting it from the trace (ASA-vers. 4.6 by ANT software).
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by the optical signal
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