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yycunc / SAMEclustering

SAME (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data
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Seurat: "Error in UpdateSlots(object = x) : argument "x" is missing, with no default" #3

Closed Fatberg closed 2 years ago

Fatberg commented 3 years ago

Hello,

I'm running the sample Zheng et al data, and the Seurat functions provide this error (v1.00):

Error in UpdateSlots(object = x) : argument "x" is missing, with no default

Command:

cluster.result <- individual_clustering(inputTags = data_SAME$Zheng.expr, percent_dropout = 10, SC3 = TRUE, CIDR = TRUE, nPC.cidr = NULL, Seurat = TRUE, nPC.seurat = NULL, resolution = 0.9, tSNE = TRUE, dimensions = 2, perplexity = 30, SIMLR = TRUE, diverse = TRUE, SEED = 123)

I'm running Seurat_4.0.1.

Fatberg commented 3 years ago

This was fixed by running the tutorial commands from Github instead of the group website:

cluster.result <- individual_clustering(inputTags = data_SAME$Zheng.expr, mt_filter = TRUE, percent_dropout = 10, SC3 = TRUE, CIDR = TRUE, nPC.cidr = NULL, Seurat = TRUE, nGene_filter = FALSE, nPC.seurat = NULL, resolution = 0.7, tSNE = TRUE, dimensions = 2, perplexity = 30, SIMLR = TRUE, diverse = TRUE, save.results = FALSE, SEED = 123)

However, 2 samples are absent from the result matrix of the tutorial dataset (works great on my own data).