Exercise

Plot PCA of log counts

Dimensionality reduction is usually performed on the log counts instead of the counts to reduce the bias towards highly expressed genes (higher counts dominate the variation levels between the cells).

Instructions

100 XP

Create a log counts variable using log1p() and assign it to logcounts.
Add logcounts as an assay to sce.
Plot PC1 and PC2 of the logcounts. The cells should be color coded by the publishedClusters found in Fletcher et al paper and shaped by Batch.

Take Hint (-30 XP)