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Code should be placed in three backticks as shown below

library(limma)
library(edgeR)
directory="/home/abhisek/Downloads/result analysis"
filess <- grep("a_gene_count_matrix.txt",list.files(directory), value = TRUE)
x <- readDGE(filess, columns=c(1,2),header=TRUE)
class(x)
dim(x)
# annotate the samples 
x$samples
#samplenames <- substring(colnames(x), 1, nchar(colnames(x)))
samplenames <- substring(colnames(x),1,2)
samplenames
colnames(x) <- samplenames
#make groups
group <- as.factor(c("CK", "CK", "CK", "LD", "LD", "LD", "MD", "MD", "MD"))
x$samples$group <- group

Question - I am working with the following .txt file which is a tab-separated file of the count of genes. but in sample annotation I can not get the name of the sample I think there is something problem in the reading of my data.

Gene count file is following -

Geneid CK1 CK2 CK3 LD1 LD2 LD3 MD1 MD2 MD3

TEA_000001 144 195 109 172 254 366 156 117 129

Output -

samplenames

[1] "a_"

Does this help explain your issue to you?

> z <- c("word", "anotherword", "ditto")
> substring(z, 1, 2)
[1] "wo" "an" "di"