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Fluorescence intensity was calculated minus the background using ImageJ National Institutes of Healthh).
The signal to noise ratio (S/N) was defined as the spot signal minus the background signal, divided by the standard deviation of the background signal.
Frequencies of Flu-specific CD8+ T cells are the result of the frequency obtained minus the background of unlabeled cells with the tetramer.
The normalized value of a spot was calculated from the spot signal minus the background level of hybridization (determined from the intensity of the signal surrounding each spot), divided by the median value of all the signals detected on the filter.
(b) Fluorescence intensities of Nef and MHC-I-VN-Flag positive cells were quantified in ImageJ, minus the background signal, to observe a decrease in fluorescence in the presence of the MHC-I mutations (n = 100, *indicates p-value < 0.05, **indicates p-value < 0.01).
Corrected intensity means the intensity of SH signal minus the background measured in the same experimental conditions.
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This means that first the intensities of Cy3 minus the Cy3 background signal for all spots and Cy5 minus the Cy5 background Cy5 signal for the MRSA252 spots were calculated.
Total spot intensity minus the surrounding background produced a corrected spot intensity.
The signal from each spot was calculated as the average intensity minus the average local background.
However, in contrast to the two-branch model, here the model is overdetermined in the sense that there are 15 non-background experimental values of i0 (the difference of mRNA outflow for a given state minus mRNA for the background state) that must be replicated by the model via adjustment of only ten model parameters vi, i = 1,..,4, and ri, i = 1,..,6.
For every particular spot the intensity of Cy3 minus the Cy3 background signal and Cy5 minus the Cy5 background signal was calculated, after which Cy3 to Cy5 ratios were calculated and log2-transformed.
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