Hello,

I am trying to use CIBERSORT to deconvolute the immune cells in pancreatic cancer after my treatments. I have 3 biological replicates of Control, Treatments A,B,C.

Using edgeR, I created the cpm matrix which is not log transformed. and converted it to the required format as follows:

# Load Packages ----
library(edgeR) 
library(org.Mm.eg.db)

# Load the data ----
data<- read.csv("gene_count_matrix.csv", header = T, row.names = 1L) # n=55401
pheno<- read.csv("pheno_sheet.csv", header = T, row.names = 1L)

# Load the data into edgeR ----
dge<- DGEList(counts=data, group = pheno$Sample) # n=55401

# Filtering low count genes ----
keep<- filterByExpr(dge)
dge<- dge[keep,,keep.lib.sizes=FALSE] # n=21476

# Normalising the data ----
dge<- calcNormFactors(dge)

cpm<- cpm(dge, log=F) # n=21476
cpm<- data.frame(cpm)
cpm$ENTREZID<- mapIds(org.Mm.eg.db, keys = rownames(cpm), keytype = "ENSEMBL", column = "ENTREZID")
cpm<- cpm[!duplicated(cpm$ENTREZID),]
cpm$SYMBOL<- mapIds(org.Mm.eg.db, keys = rownames(cpm), keytype = "ENSEMBL", column = "SYMBOL")
cpm<- na.omit(cpm)
rownames(cpm) = cpm$SYMBOL
cpm<- subset(cpm, select = -c(ENTREZID, SYMBOL))

write.csv(cpm, "CPM_CIBERSORTX.csv")

I then converted it to a tab delimited file and uploaded it to CIBERSORTx.

Using the default LM22 matrix, I used the following job parameters:

Date: 2022-10-12 14:39:40
Job type: Impute Cell Fractions
Signature matrix file: LM22.update-gene-symbols.txt
Mixture file: CPM_CIBERSORTX.txt
Batch correction: enabled
Batch correction mode: B-mode
Disable quantile normalization: true
Run mode (relative or absolute): relative
Permutations: 100

And then this is the error I got:

Error: $ operator is invalid for atomic vectors
In addition: Warning message:
In mclapply(1:svn_itor, res, mc.cores = svn_itor) :
  all scheduled cores encountered errors in user code
Execution halted

Does anyone know how to resolve this?

Thanks for your time.