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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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There is a problem in the running data #41

Open chenx9 opened 1 year ago

chenx9 commented 1 year ago

Hello, I have the following problem when dealing with my data:

  1. First of all, when I use all the data, my single cell data is 150,000, and I get the following error, I want to know if Scissor has a requirement on the number of cells. I see your proposed solution but it doesn't work for me.

Cholmod error 'problem too large' at file .. /Core/cholmod_dense.c, line 102

  1. While I was pulling out some cells for testing, I encountered the following problem while running the scissor step

infos4 <- Scissor(bulk_dataset, sc_dataset, phenotype, tag = tag, alpha = 0.5, family = "binomial", Save_file = "Scissor_LUAD_TP53_mutation.RData")

Error in array(x, c(length(x), 1L), if (! is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'

I don't know if it's because my data is integrated. I want to try to run

sc_dataset <-Seurat_preprocessing(sc_dataset, verbose = F)

I still get errors

Error in as.vector(data) : no method for coercing this S4 class to a vector

  1. There is another question I would like to consult. If I only use disease grouping as the phenotype condition, can I do not need BULK data for implementation