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Question: How to overcome "duplicate row.names" error while importing tpm/count/fpkm matrix/table in R ?
0
gravatar for sciencer
9 months ago by
sciencer • 70
sciencer • 70 wrote:

HI,

I used RSEM to produce TPM matrix for 100 RNA seq reads (row names= gene, columns are cell number) I get the following error, can anyone help me please!

> all <-read.table(file="tpm_matrix.xls",header=T)
Error in read.table(file = "tpm_matrix.xls", header = T) : 
  duplicate 'row.names' are not allowed

I changed the format of row names from "gene10000_Ermap" to "Ermap".
rna-seq R software error • 1.6k views
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modified 9 months ago by andrew.j.skelton73 ♦ 5.4k • written 9 months ago by sciencer • 70
1

If your file is rather a text file but no MS xls, you can use cut -f 1 tpm_matrix.xls | sort | uniq -c | sort -k1,1nr to find the duplicated row names. If there are only a few, you'll curate that manually; if you have a lot, you can use e.g. awk to add a consecutive number to the name.

ADD REPLY • link written 9 months ago by michael.ante • 2.9k

This helped, Thank you so much

ADD REPLY • link written 9 months ago by sciencer • 70
1
gravatar for andrew.j.skelton73
9 months ago by
andrew.j.skelton73 ♦ 5.4k
London
andrew.j.skelton73 ♦ 5.4k wrote:
library(gdata)
data.in <- read.xls("tpm_matrix.xls")

read.table is trying to create a matrix, and as you've observed duplicate row names aren't allowed. You can get around this by importing it as a data frame.

Disclaimer: Untested, and probably a Tidyverse way to do it now instead of openxlsx...

ADD COMMENT • link modified 9 months ago • written 9 months ago by andrew.j.skelton73 ♦ 5.4k

Hi, Thanks but I get the following error!

data.in <- read.xlsx("tpm_matrix.xlsx")
Error in file(con, "r") : invalid 'description' argument
In addition: Warning message:
In unzip(xlsxFile, exdir = xmlDir) : error 1 in extracting from zip file
ADD REPLY • link written 9 months ago by sciencer • 70
1

I've edited my OP - assumed it was an xlsx file, not xls... my bad.

ADD REPLY • link written 9 months ago by andrew.j.skelton73 ♦ 5.4k

tidyverse way is to use readxl. See here

ADD REPLY • link written 9 months ago by russhh • 4.1k
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