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One important usage of the shrinkage plot is a meaningful setting of low expression threshold in Low expression filter section (Figure 6). For features with low expression, the proportion of zero counts is high. Such features are less likely to be of interest in the study, and, in any case, they cannot be modeled well by a continuous distribution, such as Lognormal. Note that adding a positive offset to get rid of zeros does not help because that does not affect the error term of a lognormal model much. A high proportion of zeros can ultimately result in a drop in the trend in the leftmost part of the shrinkage plot (Figure 5).

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