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When "Lognormal with shrinkage" is enabled, a separate shrinkage plot is displayed for each design (Figure 4). First, a lognormal linear model is fitted for each gene separately, and the standard deviations of residual errors are obtained (green dots in the plot). Applying shrinkage amounts to two more steps. We look at how the errors change depending on the average gene expression and we estimate the corresponding trend (black curve). Finally, the original error terms are adjusted (shrunk) towards the trend (red dots). The adjusted error terms are plugged back into the lognormal model to obtain the reported results such as p-value.
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For instance, in Figure 5 it looks like a threshold of 2 can get us what we want. Since the x axis is on the log2 scale, the corresponding value for "Lowest average coverage" is 22=4 (Figure 6). After we set the filter that way and rerun GSA, the shrinkage plots takes the required form (Figure 7).
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Speaking of higher expression features, presently GSA has no automatic method to separate "abnormal" and "normal" features, so the user has to do some eyeballing of the shrinkage plot. However, for the purpose of investigating standalone outliers GSA can quantify the benefit of shrinkage in a well grounded way. In order to do that, one can enable both Lognormal and Lognormal with shrinkage in Advanced Options (Figure 9).
Figure 9:
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Figure 10 contains a pie chart for the dataset whose shrinkage plot is displayed in Figure 4. Because of a small sample size (two groups with four observations each) we see that, overall, shrinkage is beneficial: for an "average" feature, Akaike weight for feature-specific Lognormal is 25%, whereas Lognormal with shrinkage weighs 75%.Figure 10:
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At the same time, if we look at ERCC-00046 specifically (Figure 11) we see that Lognormal with shrinkage fits so bad that its Akaike weight is virtually zero, despite having fewer parameters than feature-specific Lognormal.
Figure 11:
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Using multimodel inference appears to be a better alternative to the ad hoc method in DESeq2 that switches shrinkage on and off all the way. Once again, it is both technically possible and emotionally tempting to automate the handling of abnormal features by enabling both Lognormal models in GSA and applying them to all of the transcripts. Unfortunately, that can make the results less reproducible overall, even though it is likely to yield more accurate conclusions about the drastically outlying features.
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