You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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?
The text was updated successfully, but these errors were encountered:
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?
The text was updated successfully, but these errors were encountered: