Hello, I'm working with DESeq2 package. When I try to run the code I get this error with the additional warning message:

Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘0’, ‘0.0011’, ‘0.0012’, ‘0.0013’, ‘0.0014’, ‘0.0015’, ‘0.0016’, ‘0.0017’, ‘0.0018’, ‘0.0019’, ‘0.002’, ‘0.0021’, ‘0.0022’, ‘0.0023’, ‘0.0024’, ‘0.0025’, ‘0.0026’, ‘0.0027’, ‘0.0028’, ‘0.0029’, ‘0.003’, ‘0.0031’, ‘0.0032’, ‘0.0033’, ‘0.0034’, ‘0.0035’, ‘0.0036’, ‘0.0037’, ‘0.0038’, ‘0.0039’, ‘0.004’, ‘0.0041’, ‘0.0042’, ‘0.0043’, ‘0.0044’, ‘0.0045’, ‘0.0046’, ‘0.0047’, ‘0.0048’, ‘0.0049’, ‘0.005’, ‘0.0051’, ‘0.0052’, ‘0.0053’, ‘0.0054’, ‘0.0055’, ‘0.0056’, ‘0.0057’, ‘0.0058’, ‘0.0059’, ‘0.006’, ‘0.0061’, ‘0.0062’, ‘0.0063’, ‘0.0064’, ‘0.0065’, ‘0.0066’, ‘0.0067’, ‘0.0068’, ‘0.0069’, ‘0.007’, ‘0.0071’, ‘0.0072’, ‘0.0073’, ‘0.0074’, ‘0.0075’, ‘0.0076’, ‘0.0077’, ‘0.0078’,  [... truncated]

My data contain gene names as row names and FPKM counts as columns. Here is my script:

library("DESeq2")
library("ggplot2")

data1 <- read.delim("TCGA-D3-A2JF_alive_male.txt", header = T, sep = "\t")
rownames(data1) = make.names(data1$gene_name, unique = T)
data1 <- subset(data1[2])
data2 <- read.delim("TCGA-D3-A3ML_dead_male.txt", header = T, sep = "\t")
rownames(data2) = make.names(data2$gene_name, unique = T)
data2 <- subset(data2[2])
data3 <- read.delim("TCGA-D9-A148_alive_male.txt", header = T, sep = "\t")
rownames(data3) = make.names(data3$gene_name, unique = T)
data3 <- subset(data3[2])
data4 <- read.delim("TCGA-EE-A180_dead_male.txt", header= T, sep = "\t")
rownames(data4) = make.names(data4$gene_name, unique = T)
data4 <- subset(data4[2])
data5 <- read.delim("TCGA-ER-A3ES_dead_male.txt", header = T, sep = "\t")
rownames(data5) = make.names(data5$gene_name, unique = T)
data5 <- subset(data5[2])
data6 <- read.delim("TCGA-FR-A3YO_alive_female.txt", header = T, sep = "\t")
rownames(data6) = make.names(data6$gene_name, unique = T)
data6 <- subset(data6[2])
data7 <- read.delim("TCGA-FS-A1ZZ_dead_female.txt", header = T, sep = "\t")
rownames(data7) = make.names(data7$gene_name, unique = T)
data7 <- subset(data7[2])
data8 <- read.delim("TCGA-FS-A4F0_alive_female.txt", header = T, sep = "\t")
rownames(data8) = make.names(data8$gene_name, unique = T)
data8 <- subset(data8[2])
data9 <- read.delim("TCGA-FW-A3R5_alive_male.txt", header = T, sep = "\t")
rownames(data9) = make.names(data9$gene_name, unique = T)
data9 <- subset(data9[2])
data10 <- read.delim("TCGA-GN-A9SD_dead_female.txt", header = T, sep = "\t")
rownames(data10) = make.names(data10$gene_name, unique = T)
data10 <- subset(data10[2])
data11 <- read.delim("TCGA-HR-A2OH_dead_female.txt", header = T, sep = "\t")
rownames(data11) = make.names(data11$gene_name, unique = T)
data11 <- subset(data11[2])
data12 <- read.delim("TCGA-RP-A6K9_alive_female.txt", header = T, sep = "\t")
rownames(data12) = make.names(data12$gene_name, unique = T)
data12 <- subset(data12[2])
countData <- cbind(data1,data2,data3,data4,data5,data6,data7,data8,data9,data10,data11,data12, deparse.level = 1)
metaData <- read.delim("metadata.txt", header = T, sep = "\t")

dds <- DESeqDataSetFromMatrix(countData = countData,
                              colData = metaData,
                              design = ~status, tidy = T)

My initial data contained duplicate row names; therefore, I tried to remove them by using make.names. After that there was no duplicates in row names, when I checked it with:

anyDuplicated(rownames(countData))

Thank you in advance.

The error message suggests that you have RPKM as row names. You can't get valid results with DESeq if you give it RPKM anyway.