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In addition to the previous output of ‘SC scaled data’ data node that are still used to perform integration, PCA, etc (Figure 3). It is a matrix of normalized values (residuals) that by default has the same size as the input data set.  The range of normalized values is roughly between -4 and 4. SCTransform v2 outputs a second data node named ‘SC corrected data’. ‘SC corrected data’ is equivalent to the ‘corrected counts’ that are stored in the data slot of the SCT assay for differential expression(DE) analyses (Figure 3). To ensure the fixed value is set properly,  the ‘PrepSCTFindMarkers’ task has also been run under the hood in Flow.  When perform DE analysis with Hurdle,  the 'shrinkage of error term variance' option might need to turn off depending on the dataset. Similarly, the 'Lognormal with shrinkage/voom' option needs to turn off when run DE with GSA.

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