Hello All, 

I have read counts from RNA seq data in row and columns. I want to quantile normalized them in R. I have following code. This gives me the normalized values. However, the output is a matrix. I want the output with row name and column name so that I can perform PCA on it. 


    data <- read.csv("data.csv",header=T)
    head(data)
    data_mat <- as.matrix(data[,-1]) 
    head(data_mat)
    data_norm <- normalize.quantiles(data_mat, copy = TRUE)


Could someone help me to get that? Thank you in advance. 
Try this (note the extra line; also use `data.matrix`, not `as.matrix`):

    data <- read.csv("data.csv",header=T)
    head(data)
    rownames(data) <- data[,1]
    data_mat <- data.matrix(data[,-1]) 
    head(data_mat)
    data_norm <- normalize.quantiles(data_mat, copy = TRUE)


