Zhu-JC
commented
1 year ago Hi herong I have the same error like you!And then I found this is because we download the wrong ExpressionSet data! You should go to 'https://xuranw.github.io/MuSiC/articles/pages/data.html' and download [Single cell RNA-seq data of pancreatic islets from healthy individuals] under SingleCellExperiment as reference dataset. best wishes!
hello,everyone, I run my code as follow: library(MuSiC2) library(MuSiC) library(bseqsc) setwd("D:/cibersortx/Music/music2")
Bulk RNA-seq data
benchmark.eset = readRDS("bulk-eset.rds") benchmark.eset
clinical conditions
table(benchmark.eset$group) bulk.control.mtx = exprs(benchmark.eset)[, benchmark.eset$group == 'healthy'] bulk.case.mtx = exprs(benchmark.eset)[, benchmark.eset$group == 't2d']
scRNA-seq data
seger.sce = readRDS("EMTABesethealthy.rds") #EMTABesethealthy.rds seger.sce
music2 deconvolution
set.seed(1234) est = music2_prop_t_statistics(bulk.control.mtx = bulk.control.mtx, bulk.case.mtx = bulk.case.mtx, sc.sce = seger.sce, clusters = 'cellType', samples = 'sampleID', select.ct = c('acinar','alpha','beta','delta','ductal','gamma'), n_resample=20, sample_prop=0.5,cutoff_c=0.05,cutoff_r=0.01)
An error in music2_prop_t_statistics function as follows: est = music2_prop_t_statistics(bulk.control.mtx = bulk.control.mtx, bulk.case.mtx = bulk.case.mtx, sc.sce = seger.sce, clusters = 'cellType', samples = 'sampleID', select.ct = c('acinar','alpha','beta','delta','ductal','gamma'), n_resample=20, sample_prop=0.5,cutoff_c=0.05,cutoff_r=0.01) Error in h(simpleError(msg, call)) : 在为'['函数选择方法时评估'j'参数出了错: no slot of name "colData" for this object of class "ExpressionSet" ,how can we solve the proplom?