While playing with the example provided online, I got a question and need your help. Below is the workflow:
all.counts <- as.data.frame(read_excel("D:\\HDexamples\\GSE61533_HTSEQ_count_results.xls", sheet=1))
rownames(all.counts) <- all.counts$ID
all.counts <- as.matrix(all.counts[,-1])
library(SingleCellExperiment) # installed from local file download
sce <- SingleCellExperiment(assays=list(counts=all.counts))
is.spike <- grepl("^ERCC", rownames(sce))
isSpike(sce, "ERCC") <- is.spike
is.mito <- grepl("^mt-", rownames(sce))
sce <- calculateQCMetrics(sce, feature_controls=list(ERCC=is.spike, Mt=is.mito))
Error in calculateQCMetrics(sce, feature_controls = list(ERCC = is.spike, :
object must be an SCESet object.
Package "scater" was installed a few days ago.