finding error to run edgeR, error in ploting MDS and after that in model matrix also

finding error to run edgeR, error in ploting MDS and after that in model matrix also

0

library(edgeR)
counts <- read.delim(“GSE116959_series_matrix.txt”, row.names = 1)
head(counts)
d0 <- DGEList(counts)
d0 <- calcNormFactors(d0)
d0
cutoff <- 1
drop <- which(apply(cpm(d0), 1, max) < cutoff)
d <- d0[-drop,]
dim(d) # number of genes left
snames <- colnames(counts) # Sample names
snames
sample <- substr(snames, 1, nchar(snames) – 2)
sample_no <- substr(snames, nchar(snames) – 1, nchar(snames) – 1)
sample
sample_no
group <- interaction(sample, sample_no)
group
plotMDS(d, col = as.numeric(group))
mm <- model.matrix(~0 + group)
y <- voom(d, mm, plot = T)


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