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Question: Error from scater package
0
gravatar for huiyunwu
5 weeks 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 5 weeks ago by Aaron Lun17k • written 5 weeks ago by huiyunwu0

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Peter Hickey290
0
gravatar for Aaron Lun
5 weeks ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k 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 5 weeks ago by Aaron Lun17k
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