Repeated tag sequence error
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@e49ee5f8
Last seen 9 days ago
India

Enter the body of text here I am using edgeR for RNA seq analysis, repeated tag sequence error was obtained frequently. Kindly help me in this regard.

Code should be placed in three backticks as shown below


>     x <- readDGE(files, columns=c(1,2))

Error in readDGE(files, columns = c(1, 2)) : 
  Repeated tag sequences inGSM4321761_WT_rep1.txt

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
edgeR • 187 views
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You apparently have duplicates in your input file. Did you see this post? It provides some ways to check this. edgeR import error

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Yes Sir, I have seen that post. I am using R for the first time. I am not able to debug the error with the code x <- read.delim("tmp1.txt", stringsAsFactors = FALSE) any(duplicated(x[,1])). Kindly provide me suggestions.

x <- readDGE(files, stringAsfactors=FALSE)

Error in read.table(file = file, header = header, sep = sep, quote = quote, : unused argument (stringAsfactors = FALSE)

x <- read.delim("GSM4321761_WT_rep1.txt", stringsAsFactors = FALSE) any(duplicated(x[,1])) [1] TRUE

x[duplicated(x[,1]),] tracking_id FPKM 11616 LOC_Os02g55670 7.75375 28033 LOC_Os06g07923 12.15650 45853 LOC_Os10g22310 0.00000 46591 LOC_Os10g31460 15.15640 46593 LOC_Os10g31460 54.53610

x <- readDGE(files) Error in readDGE(files) : Repeated tag sequences inGSM4321761_WT_rep1.txt

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@gordon-smyth
Last seen 19 minutes ago
WEHI, Melbourne, Australia

The problem is not with the R code but with the data you are trying to read.

I am going to guess that you are trying to read files from the GEO series GSE145579: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145579

The data provided by this GEO series contains two fatal errors:

  • First there are multiple rows with the same feature names (tracking_id) as previous rows, which is nonsense and prevents one from making sense of the data. This is the problem that has been correctly diagnosed by the edgeR readDGE function.
  • Second, the data provides FPKM values rather than read counts and FPKM values cannot be analysed using edgeR. FPKM values are unfortunately unsuitable for downstream differential expression analyses.

I suggest that you write to the authors of the GEO study and ask them to provide you with data in a more useful form.

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