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I have RNA-seq Data from lung cancer immunotherapy patients but i don't have any single cell data from my sample, so i wanted to do a deconvolution with a public single cell data. I thought of doing the analysis with the cibersort website plataform but i wanted to obtain the results in R, to be easy to work with them.So i followed the steps in this article, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895181/ :

library(e1071)
library(parallel)
library(preprocessCore)
source("CIBERSORT.R")
results <- CIBERSORT(‘sig_matrix_file.txt’, ‘mixture_file.txt’, perm=100, QN=TRUE)

But in when i did source("CIBERSORT.R"), i obtain this:

"Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'CIBERSORT.R': No such file or directory"

I don't understand i was supposed to have a file?

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  • $\begingroup$ Is the R script available on the Cibersort website? I was looking for it some time ago but couldn't find. I don't have my credentials for the site on this computer so can't check now. $\endgroup$
    – Cloudberry
    Oct 24, 2023 at 16:49

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