I'm learning how to do simple analysis to single cell sequencing data from this workflow http://bioconductor.org/help/workflows/simpleSingleCell/#denoising-expression-values-using-pca#cmid=172561
In the QC step, it used the function calculateQCMetrics. But I got warning: Error in calculateQCMetrics(sce, feature_controls = list(ERCC = is.spike, : object must be an SCESet object.
sce is defined as SingleCellExperiment object because it will use colData() function of SingleCellExperiment in the following step. Thus, there seems no way to change sce from SingCellExperiment to SCESet object. I know this is not a problem in the older version of Scater package, so SingleCellExperiment object cannot be used by Scater package now?