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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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Slingshot error #248

Open Leoarie-lab opened 6 months ago

Leoarie-lab commented 6 months ago

Dear everyone,

I run this commands

DefaultAssay(today) <- "RNA" sce <- as.SingleCellExperiment(today, assay = "RNA")

sce <- slingshot(sce, reducedDim = "WNN.UMAP", clusterLabels = colData(sce)$ident,start.clus = "Classical", approx_points = 150,useNames = TRUE)

But it showed the error that Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

Even I put useNames in FALSE or TRUE.

I am sorry, I am new for R or running pseudo time. Could anyone help me to resolve this error?

Thank you very much.

sce class: SingleCellExperiment dim: 36601 8319 metadata(0): assays(2): counts logcounts rownames(36601): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2 rowData names(0): colnames(8319): AAACCTGAGAACAACT-1 AAACCTGAGAGCAATT-1 ... TTTGTCATCGACCAGC-1 TTTGTCATCTCGTATT-1 colData names(11): orig.ident nCount_RNA ... seurat_clusters ident reducedDimNames(3): PCA APCA WNN.UMAP mainExpName: RNA altExpNames(0):

kstreet13 commented 6 months ago

Hi @Leoarie-lab,

Thanks for your comment! That error message is a bit confusing, because it's not actually coming from the slingshot function, but some other function that gets called by slingshot. This has come up a few times before (notably here) and you should be able to get rid of it by updating a few packages to the latest versions, including slingshot, Matrix, and matrixStats (this may also require updating to the latest version of R, if you haven't already). You will also need to remove the argument useNames = TRUE, otherwise this will cause an error due to the fact that useNames is not a valid argument to the slingshot function.

Hope this helps! Kelly