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Figure 7: Quality of the automated gating was assessed by performing a robust logistic regression of the percentage of cells above the isotype gate on the log transformed MFI ratio and looking for estimates that were more than 2 standardized residuals away from the best fit line (red line). There were 18 estimates flagged in this study (red diamonds) where the value was different than we would predict from the MFI ratio. Detailed examination of these 18 cases showed that the isotype gate settings were reasonable, but they differed from other markers in that they had more than one population of stained cells. Sample density plots for one of these markers, CD3, are provided in Figure 8.