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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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Error in hclust(md, method = "ward.D2") : Invalid clustering method " #1

Closed cdkodira closed 2 years ago

cdkodira commented 4 years ago

I get this error " Error in hclust(md, method = "ward.D2") : Invalid clustering method "

when I run this command- cluster.result <- individual_clustering(inputTags = data_SAME$Zheng.expr, datatype = "count", 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)

yycunc commented 4 years ago

Hi,

Thanks for interesting in our method. I think the issue occurs when you call CIDE for clustering. May I have some more details on your data? What is the cell number for the expression matrix?

cdkodira commented 4 years ago

I'm using your example file. Thanks, Dilip

cluster.results <- individual_clustering(inputTags = data_SAFE$Zheng.expr, datatype = "count", mt_filter = FALSE, CIDR = TRUE, nPC.cidr = NULL, Seurat = TRUE, nPC.seurat = NULL, resolution = 0.9, nGene_filter = FALSE, SC3 = TRUE, gene_filter = FALSE, tSNE = TRUE, dimensions = 3, perplexity = 30, SEED = 123)

Performing SC3 clustering... Estimating k... Setting SC3 parameters... Calculating distances between the cells... Performing transformations and calculating eigenvectors... Performing k-means clustering...

Calculating consensus matrix... Performing CIDR clustering... Performing Seurat clustering... Error in CreateSeuratObject(raw.data = inputTags, min.cells = 3, min.genes = 200, : unused arguments (raw.data = inputTags, min.genes = 200)

From: yycunc notifications@github.com Sent: Thursday, June 18, 2020 12:20 PM To: yycunc/SAMEclustering SAMEclustering@noreply.github.com Cc: cdkodira cdkodira@hotmail.com; Author author@noreply.github.com Subject: Re: [yycunc/SAMEclustering] Error in hclust(md, method = "ward.D2") : Invalid clustering method " (#1)

Hi,

Thanks for interesting in our method. I think the issue occurs when you call CIDE for clustering. May I have some more details on your data? What is the cell number for the expression matrix?

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yycunc commented 4 years ago

Hi Dilip,

According to the error information, I think it occurs that you are using the latest Seurat version (v3 or higher), however, SAMEclustering works with Seurat v2. Now, the way to fix it is to run individual_clustering function with Seurat = FALSE, and run Seurat separately, and then combined the clustering outputs together for downstream cluster ensemble.

I also want to thank you for the comments. As more and more people use Seurat v3 now, I will update the individual_clustering function to make it compatible to Seurat v3.