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IMB-Computational-Genomics-Lab / ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)
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error in scranNormalise(em.set) #6

Closed jonxujun closed 6 years ago

jonxujun commented 6 years ago

met an error in scranNormalise(em.set) following the vignette:

norm.set <- scranNormalise(em.set) [1] "Converting EMSet to SCESet..." Error in seq_len(ncol(assay)) : argument must be coercible to non-negative integer In addition: Warning messages: 1: 'newSCESet' is deprecated. Use 'SingleCellExperiment' instead. See help("Deprecated") 2: In seq_len(ncol(assay)) : first element used of 'length.out' argument

This error is not there when I do not skip the cell cycle identification step: em.set <- ConvertGeneAnnotation(em.set, "gene_symbol", "ensembl_id") training.data <- readRDS(system.file("exdata", "human_cycle_markers.rds", package = "scran")) em.set <- scranCellCycle(em.set, training.data) cell.info <- GetCellInfo(em.set) cell.info[1:5, ] em.set <- ConvertGeneAnnotation(em.set, "ensembl_id", "gene_symbol")

asenabouth commented 6 years ago

This is an issue with SingleCellExperiment replacing SCESets in the latest version of Bioconductor. Currently working on a conversion function to address this. Thanks for flagging.

asenabouth commented 6 years ago

Fixed in update 8c9bc8260109cdde2e4ff7e06aef0473898d962e