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Problem with newSCESet(countData=all.counts) function

Hi, I m running through this for single cell RNAseq data analysis. And I got this error after running a few codes. If some one could figure out that what might have I done wrong, I will appreciate. Thanks

library(R.utils)
gunzip("GSE61533_HTSEQ_count_results.xls.gz", remove=FALSE, overwrite=TRUE)
library(gdata)
all.counts <- read.xls(’GSE61533_HTSEQ_count_results.xls’, sheet=1, header=TRUE, row.names=1)
library(scater)

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SingleCellExperiment", version = "3.8")

library(SingleCellExperiment)
sce <- newSCESet(countData=all.counts)

Error in newSCESet(countData = all.counts) : 
  could not find function "newSCESet"
single cell experiment single cell rna seq
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updated by Santosh Anand Santosh Anand • written by bk11 • bk11

Very strange! Check again in a fresh R-session, especially double check that scater library is loaded

library(scater)

• 1 views • link
written by Santosh Anand Santosh Anand

Thank you Santosh. library(scater) was loaded and still could not find function "newSECSet"

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written by bk11 • bk11

1 answer

Scater has switched to SingleCellExperiment object and SCESet has been removed from new scater releases.

https://support.bioconductor.org/p/101956/

See the latest doc on how SingleCellExperiment works

https://bioconductor.org/packages/release/bioc/vignettes/scater/inst/doc/vignette-intro.html

See also the workflow for single cell analysis

http://master.bioconductor.org/packages/release/workflows/html/simpleSingleCell.html

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written by Santosh Anand Santosh Anand

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