DSEQ for DEG in R
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amoaristotle ▴ 10
@user-24704
Last seen 7 months ago

I have more than 2500 candidate gene and i want to use transcriptomic data from a database to check for their differential expression.

So am using the following code

#just.raw.counts = read.delim("Raw_counts_input.txt", row.names=1)

#meta.data = read.delim(file="meta_data.txt", row.names = 1)

#count.data.set <- DESeqDataSetFromMatrix(countData=just.raw.counts, 
    colData=meta.data, design= ~ condition)

however, when I try to run the first code I get an error

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

Below is the count data format and coldata format

transcript  Control_R1  Control_R2  Control_R3  Day1_R1 Day1_R2 Day1_R3 Day2_R1 Day2_R2 Day2_R3 Day3_R1 Day3_R2 Day3_R3 Day5_R1 Day5_R2 Day5_R3
TraesCS1A02G007700.1    0   1   0   0   0   0   0   0   0   0   0   0   0   0   0
TraesCS1A02G007800.1    19  30  26  13  8   1   10  10  19.4163 21  17  16  27  32  18
TraesCS1A02G007900.1    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0


    condition
Control_R1  Control
Control_R2  Control
Control_R3  Control
Day1_R1 Day1
Day1_R2 Day1
Day1_R3 Day1
Day2_R1 Day2
Day2_R2 Day2
Day2_R3 Day2
Day3_R1 Day3
Day3_R2 Day3
Day3_R3 Day3
Day5_R1 Day5
Day5_R2 Day5
Day5_R3 Day5

Please how can I solve this?

microbiomeExplorer tartare projectR • 212 views
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