Problem with newSCESet(countData=all.counts) function

Question

[bk11]

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"

[Santosh Anand]

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

library(scater)

[bk11]

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

Answer 1

[Santosh Anand]

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