Hi there,

While playing with the example provided online, I got a question and need your help. Below is the workflow:

Source:

https://www.bioconductor.org/help/workflows/simpleSingleCell/

Code:

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))

library(scater)
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.

Thanks,

William Wu

The workflows have been updated to Bioconductor 3.6 in preparation for the upcoming release. If you want to use the code on the workflow page, you need to upgrade to BioC-devel for the time being.

library(BiocInstaller)
useDevel()
biocLite()