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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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Error: in normalize.quantiles(dataset0): vector types do not match in copyVector #51

Open rln0005 opened 1 year ago

rln0005 commented 1 year ago

I am having an issue using Scissor to annotate bulk RNA sequencing (of paired tumor & normal samples) with single-cell tumor sequencing.

Here is my code:

## import bulk RNA seq data
bulk <- as.matrix(read.csv("gene_count_matrix.csv"))
# convert the bulk dataset to matrix
bulk_dataset <- as.matrix(bulk_dataset)

## import bulk phenotype data
pheno <- read.table("Scissor_pheno.txt")

## import single-cell multiome seq data
sc <- Read10X_h5('C:/path/to/filtered_feature_bc_matrix.h5')
sc <- sc$`Gene Expression`
# perform seurat pre-processing 
sc_dataset <- Seurat_preprocessing(sc)

## run Scissor function 
phenotype <- pheno
tag <- c('Normal', 'Tumor')
info <- Scissor(bulk_dataset, sc_dataset, phenotype, tag=tag, alpha=0.5, family="binomial")

This results in the following error: 

Error in normalize.quantiles(dataset0) : 
  vector types do not match in copyVector

I have tried several different things (including manual installation of preprocessCore, using BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE) ...but nothing has worked. I also had issues with the normalize.quantiles() before I coerced the bulk dataset into a matrix.

Can someone advise on if I've made an error, and/or how to mitigate this issue?

Able-Andy commented 1 year ago

Have you figured this problem? I got the same problem as you.

rln0005 commented 1 year ago

No, I haven't been able to figure this out.

Have you figured this problem? I got the same problem as you.

Able-Andy commented 1 year ago

Hi，I‘ve solved this problem, maybe the forms of input bulk_dataset and phenotype are wrong, the form of phenotype is "named num". Also, my problem is my bulk_dataset ,maybe there are some errors when I got my bulk. You can see this 'https://www.zhblog.net/qa/object-class-r.html' ,hoping it will help.

No, I haven't been able to figure this out.

Have you figured this problem? I got the same problem as you.

NIKO6666666 commented 6 months ago

Hi，I‘ve solved this problem, maybe the forms of input bulk_dataset and phenotype are wrong, the form of phenotype is "named num". Also, my problem is my bulk_dataset ,maybe there are some errors when I got my bulk. You can see this 'https://www.zhblog.net/qa/object-class-r.html' ,hoping it will help.

No, I haven't been able to figure this out.

Have you figured this problem? I got the same problem as you.

I can't open this link, it seems to indicate a risk of privacy breach. Can you tell me the correct phenotype format and bulk matrix format? Thank you very much