Question: row names change in normalization
0
gravatar for rhasanvandj
25 days ago by
rhasanvandj20
rhasanvandj20 wrote:

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 • 104 views
ADD COMMENTlink written 25 days ago by rhasanvandj20

Hi, can you post the code you used?

ADD REPLYlink written 25 days ago by rpolicastro2.3k

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
ADD REPLYlink modified 25 days ago by RamRS30k • written 25 days ago by rhasanvandj20
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