sctransform_endocrinogenesis_day15_hackathon

The results of sctransfrom are stored in layers with the “SCT” prefix. SCT_normalized contains the residuals (normalized values), and is used directly as input to PCA. To assist with visualization and interpretation. we also convert Pearson residuals back to ‘corrected’ UMI counts. You can interpret these as the UMI counts we would expect to observe if all cells were sequenced to the same depth. The ‘corrected’ UMI counts are stored in <code>SCT_corrected_UMI</code>. We store log-normalized versions of these corrected counts in <code>SCT_lognorm_corrected_UMI</code>, which are very helpful for visualization.You can use the corrected log-normalized counts for differential expression and integration. However, in principle, it would be most optimal to perform these calculations directly on the residuals (stored in the <code>SCT_normalized</code> slot) themselves.