Hi @ioer0417,
Welcome to the RStudio Community Forum.
It is best to avoid storing "important information" from your data in the data frame row names - better to keep it in a named column for future use (e.g. splitting it to form factors). Row names, by default, are allocated numbers from 1, so remain unique.
So, try reading your data like this:
cst <- read.csv("~/R/210825_DH_deseq.csv", header = TRUE, sep = ",")
cst
If your header row has only 3 fields while the data has 4, then I suggest you ignore the header row when reading, and add it later manually:
cst <- read.csv("~/R/210825_DH_deseq.csv", header = FALSE, skip = 1, sep = ",")
cst
names(cst) <- c("id", "var1", "var2", "var3")