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An error in music2_prop_t_statistics function #103

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herong2006 opened this issue Oct 28, 2022 · 1 comment
Open

An error in music2_prop_t_statistics function #103

herong2006 opened this issue Oct 28, 2022 · 1 comment

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@herong2006
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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?

@Zhu-JC
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Zhu-JC commented Nov 24, 2022

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!

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