duplicate 'row.names' are not allowed

Question

[PK]

I have RNA-SEQ data i wanted to do DESeq (DEseq2 i am using). When i try to open my file it shows duplicate 'row.names' are not allowed like that. I already have gone through all kinds of possible ways which were discussed before but nothing worked.

This is my data

Tb927_01_v5.1     54039 54154   Novel   0   +   28     123  1   101 96  16  155 27  14  9   11

(I just highlighted every alternative tabs for your vision. I am not able to represent my data in a nice way sorry for that)

[WouterDeCoster]

This must be one of the times when R error message are actually accurate and tell you what's wrong :')

You tell R to take column 1 as row names (row.names=1)
R tells you that there are duplicates in those row names

[ATpoint]

What file is that? A count matrix? Please give some more details.

[PK]

I am trying to find some new novel transcript from my sequencing file so i did multicov from bed tools to get the read counts. bedtools multicov -bams DS1.bam DS2.bam -bed transcript_I.bed > all_transcripts_I.tsv From that i took multicov output as a DESeq2 input file (all_transcripts_I.tsv).

R function i Uesd : countdata <- read.table("file5.tsv", header=TRUE, row.names=1)

The error i got : Error in read.table("file5.tsv", header = TRUE, row.names = 1) : duplicate 'row.names' are not allowed

My input file:

Tb927_01_v5.1   55903   56066   Novel_2 0   -   8   0   29  115 57  83  42  465 41  6   8   2
Tb927_01_v5.1   74188   74343   Novel_3 0   +   0   29  265 5   249 326 41  326 106 143 65  23
Tb927_01_v5.1   83979   84150   Novel_4 0   +   0   64  16  44  103 39  20  107 27  37  8   20
Tb927_01_v5.1   85231   85459   Novel_5 0   -   10  166 490 96  746 523 1186    1611    1384    809 511 216
Tb927_01_v5.1   90185   90292   Novel_6 0   +   0   25  118 2   81  117 13  131 33  33  21  7

[EagleEye]

Because your rownames (First row) are same and you asked R to read the file by considering first row as rownames (row.names=1). Because of indexing issue R cannot take same name for multiple rows.

In your case it looks like your fourth column seems to be non-repetitive. You can consider using row.names=4

[cpad0112]

@OP: remove row.names=1.

[zx8754]

Please provide reproducible example data, maybe paste output of dput(head(MyData)). Also, post the command you are using that is causing the error.

[EagleEye]

Report the R function you used to read your file. Also provide exact error message.

[PK]

R function i Uesd : countdata <- read.table("file5.tsv", header=TRUE, row.names=1)

The error i got : Error in read.table("file5.tsv", header = TRUE, row.names = 1) : duplicate 'row.names' are not allowed

Answer 1

[Benn]

The question is also duplicate

How To Deal With Duplicate Row Names Error In R

Answer 2

[Prakash]

If you still want to use first column as rownames , use Check.name= FALSE

Answer 3

[paul.boisseaux]

If it can help someone: I had the same error message:

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  duplicate 'row.names' are not allowed

when importing my file :

phenodata = "C:/Users/.../phenodata.txt"
read.delim(phenodata, row.name=1)

The .txt file was beforehand generated from Excel. I don't know why but there was a bug: you just have to copy-paste in excel your matrix to a new excel sheet, then to convert to a .txt file and re-try the import process. It should work ! Good luck,

[Gema Sanz]

Thank you! This solved my problem

Answer 4

[bruce.moran]

R will not allow you to have rownames that are the same for each row. Using a rowname in the first place is unnecessary. There is, IMHO, a better convention for data handling in R.

Install the 'tidyverse', load the library, read the count data into a tibble. The R 'base' offers a lot, but so does 'tidyverse'. Beginners should at least be aware of and try it out, and also try to understand what 'tidy' data looks like, and why it might be a good idea.

install.packages('tidyverse') 
library('tidyverse') 
countdata <- read_tsv("file5.tsv")