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Currently, GSA is capable of considering the following five response distributions: Normal, Lognormal, Lognormal with shrinkage, Negative Binomial, Poisson (Figure 1). The GSA interface has an option to restrict this pool of distributions in any way, e.g. by specifying just one response distribution. The user also specifies the factors that may enter the model (Figure 2A) and comparisons for categorical factors (Figure 2B).
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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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A) Average expression threshold can be raised to get rid of low expression features with abnormal error terms, circled in blue
B) Six low expression features (circled in blue) account for a very sharp increase in the trend which can have an unduly large effect on overall results |
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