Update cell-cycle.Rmd

- `scRNAseq::LengESCData()` again produces an SCE with assay named 'normcounts'. - See LTLA/scRNAseq#50 (comment) and LTLA/scRNAseq@4fc723c
OSCA-source · Apr 22, 2024 · 843ada7 · 843ada7
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commit 843ada7
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/inst/book/cell-cycle.Rmd b/inst/book/cell-cycle.Rmd
@@ -318,7 +318,7 @@ library(scRNAseq)
 sce.leng <- LengESCData(ensembl=TRUE)
 
 # Performing a default analysis without any removal:
-sce.leng <- logNormCounts(sce.leng, assay.type="normalized")
+sce.leng <- logNormCounts(sce.leng, assay.type="normcounts")
 dec.leng <- modelGeneVar(sce.leng)
 top.hvgs <- getTopHVGs(dec.leng, n=1000)
 sce.leng <- runPCA(sce.leng, subset_row=top.hvgs)