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row names change in normalization

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

rna-seq
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written by Rob • Rob

Hi, can you post the code you used?

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written by rpolicastro rpolicastro

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
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updated by Ram Ram • written by Rob • Rob

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