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Question: Error from scater package
0
gravatar for huiyunwu
4 months ago by
huiyunwu0
huiyunwu0 wrote:

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

ADD COMMENTlink modified 4 months ago by Aaron Lun18k • written 4 months ago by huiyunwu0

Please include the output of sessionInfo() in your question (http://www.bioconductor.org/help/support/posting-guide/)

ADD REPLYlink modified 4 months ago • written 4 months ago by Peter Hickey320
0
gravatar for Aaron Lun
4 months ago by
Aaron Lun18k
Cambridge, United Kingdom
Aaron Lun18k wrote:

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()
ADD COMMENTlink written 4 months ago by Aaron Lun18k
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