Thanks for the useful deconvolution tool. I am trying to use TED to deconvolute bulk RNA-seq data from tissues. And I used raw reads for scRNA-seq and expected counts generated from RSEM for bulk RNA-seq as input to run TED. However, I got the error as the following:
[1] "removing non-numeric genes..."
[1] "removing outlier genes..."
Number of outlier genes filtered= 7
[1] "aligning reference and mixture..."
[1] "No tumor reference is speficied. Reference profiles are treated equally."
[1] "run first sampling"
current sample ID:1 Error in rmultinom(n = 1, size = X.i[g], prob = prob.mat[, g]) :
invalid second argument 'size'
Calls: run.Ted ... draw.sample.gibbs -> mclapply -> lapply -> FUN -> sample.n -> rmultinom
Execution halted
Here is my code :
library(TED)
ref.dat <- read.csv("scRNA-counts-for.t-for.csv", header=TRUE, row.names=1, sep="\t")
X <- read.csv("placenta_genename-count.uniq.t.for.csv", header=TRUE, row.names=1, sep="\t")
cell.type <- read.csv("scRNA-celltype-for.csv", header=FALSE, sep="\t")
cell.type.labels <- cell.type[[1]]
run.Ted(ref.dat, X, cell.type.labels, input.type="scRNA", pdf.name="trail.pdf")
Is there any suggestion about this error?
Thanks~
Thanks for the useful deconvolution tool. I am trying to use TED to deconvolute bulk RNA-seq data from tissues. And I used raw reads for scRNA-seq and expected counts generated from RSEM for bulk RNA-seq as input to run TED. However, I got the error as the following:
Here is my code :
library(TED)
Is there any suggestion about this error?
Thanks~