row names change in normalization

Question

[Rob]

Hello friends I have a problem with R. I change my data file and use rlog() in Deseq2 to normalize and log transform my data. When I normalize my data in the resulted file the first column which is my gene names turns into numbers(1, 2, 3, 4, ....) What should I do to avoid this? I want to keep the gene names in the first column.

Thanks

[rpolicastro]

Hi, can you post the code you used?

[Rob]

Thanks Here is my code:

mat <- read.table("mydata.txt", sep = '\t',
                  header = TRUE, row.names = 1, stringsAsFactors = FALSE, check.names=FALSE)
mat1 <- as.matrix (mat)
####################normalize and log2transform
mat2 <- rlog(mat1)
###### here row names change