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TRAjectory-based Differential Expression analysis for SEQuencing data
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Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments. #254

Closed chungsai closed 1 week ago

chungsai commented 4 months ago

Hello I am doing the vignette code by code

of here https://kstreet13.github.io/bioc2020trajectories/articles/workshopTrajectories.html https://github.com/kstreet13/bioc2020trajectories/blob/master/vignettes/workshopTrajectories.Rmd However, as I get to this point

set.seed(3)
icMat <- evaluateK(counts = as.matrix(assays(sce)$counts),
                   pseudotime = colData(sce)$slingshot$pseudotime,
                   cellWeights = colData(sce)$slingshot$cellWeights.V1,
                   conditions = factor(colData(sce)$pheno$treatment_id),
                   nGenes = 300,
                   k = 3:7)

I get error

Error in .local(counts, ...) : Either provide the slingshot object using the sds argument, or provide pseudotime and cell-level weights manually using pseudotime and cellWeights arguments.

print(sce) class: SingleCellExperiment dim: 10549 9268 metadata(1): tradeSeq assays(1): counts rownames(10549): AP006222.2 SAMD11 ... AC011043.1 AL592183.1 rowData names(2): tradeSeq assocRes colnames(9268): AAACATACGAATAG-1_Mock_TGFB_agregated_samples AAACATACGCTAAC-1_Mock_TGFB_agregated_samples ... TTTGCATGAAGTAG-4_Mock_TGFB_agregated_samples TTTGCATGCTGAGT-4_Mock_TGFB_agregated_samples colData names(6): pheno tradeSeq ... slingPseudotime_1 slingPseudotime_1 reducedDimNames(1): UMAP mainExpName: NULL altExpNames(0):

print(SlingshotDataSet(sce)

  • ) class: SlingshotDataSet

Samples Dimensions 9268 2

lineages: 1 Lineage1: inner outer

curves: 1 Curve1: Length: 21.008 Samples: 9268

And I cannot move forward

Session info ────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.2 (2023-10-31) os macOS Ventura 13.0 system aarch64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Toronto date 2024-02-21 rstudio 2023.12.1+402 Ocean Storm (desktop) pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

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[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

V ── Loaded and on-disk version mismatch.

koenvandenberge commented 1 week ago

Hi @chungsai

The code you refer to is from a workshop from 4 years ago, and we are no longer maintaining the code of that workflow. Our apologies.