Question

Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2

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corellig ▴ 10

@corellig-23789

Last seen 4.5 years ago

Hallo, I am working with DeSeq2 package. When I am trying to create the DeSeq matrix needed for starting the analysis, I get this error:

Error in `.rowNamesDF<-`(x, value = value) :duplicate 'row.names' are not allowed

even if online I found other posts with this problem, the solutions did not help me. When I do any(duplicated(rownames(x)))for both tables used for ColData and CountData, I get FALSE

In addition to the error I also get a warning message

In addition: Warning message:
non-unique values when setting 'row.names': ‘0’, ‘1’, ‘10’, ‘100’, ‘101’, ‘102’, ‘103’, ‘104’, ‘105’, ‘106’, ...

Here is my script:

       library(limma) 
       library(edgeR)
       library(DESeq2)
       library(ggplot2)
       library(dplyr)

    forcountdata<-read.csv("/home/student/Desktop/gene_read_counts_table_all_final_no_gene_name.csv",header=T,sep="", row.names = 1)

    colnames(forcountdata)<-c("Col0.1", "Tbl29.1","Max4.1","TM.1","Col0.2","Tbl29.2","Max4.2","TM.2","Col0.3","Tbl29.3","Max4.3","TM.3")

    metadata<-read.table("/home/student/Desktop/metadata.csv", header=T, sep=",")

    rownames(metadata)<-c("Col0.1", "Tbl29.1","Max4.1","TM.1", "Col0.2","Tbl29.2","Max4.2","TM.2","Col0.3","Tbl29.3","Max4.3","TM.3")

    rownames(metadata)==colnames(forcountdata)
    fourcountdata<-as.matrix(forcountdata)

    dds <- DESeqDataSetFromMatrix(forcountdata,
                              colData = metadata, design=(~Condition), tidy=TRUE) #Condition is inside metadata and is a column name

    any(duplicated(rownames(metadata)))
    any(duplicated(rownames(forcountdata)))

Thank you in advance!

deseq2 rownames • 5.5k views

ADD COMMENT • link updated 3.3 years ago by Michael Love 43k • written 4.5 years ago by corellig ▴ 10

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the colnames of the counts are the colnames of forcountdata:

colnames(forcountdata)<-c("Col0.1", "Tbl29.1","Max4.1","TM.1","Col0.2","Tbl29.2","Max4.2","TM.2","Col0.3","Tbl29.3","Max4.3","TM.3")

that must be the same names of the rownames of the metadata table (colnames CountData == rownames ColData), according to what DESeq tutorials/instructions say.

I do not really understand the warning message... because the rownames are not repeated as this warning says... And it counts from 1 to 10 to 100 and then it goes on and I do not understand that

The rownames of fourcountdata are the gene names from the gene library:AT1G01040, AT1G01046, etc...

ADD REPLY • link 4.5 years ago corellig ▴ 10

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Oops, I meant to ask about rownames of counts.

ADD REPLY • link 4.5 years ago Michael Love 43k

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Hi! Any updates on this Michael Love? I have the same problem. If I use a count matrix with the gene names (row names) in the first column it runs, but I'm not sure if the results are accurate. I'm using R version 4.0.5 and deseq2 version 1.30.1

ADD REPLY • link 3.3 years ago Sebastian ▴ 10

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I never heard back from the original poster after asking about rownames.

Maybe make a new post and see the posting guidelines about providing code:

http://bioconductor.org/help/support/posting-guide/#composing

ADD REPLY • link 3.3 years ago Michael Love 43k

score 0 · Answer 1 · 2020-07-02

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Michael Love 43k

@mikelove

Last seen 2 days ago

United States

What are the colnames of the counts? It looks like the warning is giving you a clue what is going on.

ADD COMMENT • link 4.5 years ago Michael Love 43k

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My advice is to keep looking around at these objects, R is just telling you that you have an issue with the rownames and you should be able to find it with some sleuthing.

One thing i saw in your code is a typo:

    fourcountdata<-as.matrix(forcountdata)

did you mean to put a u there? then you don't end up using the matrix version when you pass to DESeqDataSetFromMatrix

ADD REPLY • link 4.5 years ago Michael Love 43k