Error, cannot determine column index for replicate name

[Yinjie Qiu]

Hi all,

I used RSEM to generate a expression matrix, shown below: 

  "FT1_1" "FT1_2" "FT1_3" "FT2_1" "FT2_2" "FT2_3" "WT1_1" "WT1_2" "WT1_3" "WT2_1" "WT2_2" "WT2_3"

"Gene.100000::c200882_g1_i1::g.100000" 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 23.00 0.00 0.00 8.00

when I run ./run_DE_analysis.pl --m output_name.counts.matrix --method edgeR --samples_file samples_file.txt  

using samples_file

Cond1 FT1_1

Cond1 FT1_2

Cond1 FT1_3

Cond2 WT1_1

Cond2 WT1_2

Cond2 WT1_3

Cond3 FT2_1

Cond3 FT2_2

Cond3 FT2_3

Cond4 WT2_1

Cond4 WT2_2

Cond4 WT2_3

The error msg popped out saying 

Error, cannot determine column index for replicate name [FT2_1]$VAR1 = {

          '"FT2_2"' => 5,

          '"WT1_3"' => 9,

          '"FT2_3"' => 6,

          '"WT2_3"' => 12,

          '"FT2_1"' => 4,

          '"WT2_2"' => 11,

          '"FT1_3"' => 3,

          '"FT1_2"' => 2,

          '"WT2_1"' => 10,

          '"WT1_2"' => 8,

          '"WT1_1"' => 7,

          '"FT1_1"' => 1

        };

Can anyone help me figure out what's going on?

Thanks,

Yinjie 

[Brian Haas]

Hi,

When I've seen this happen before where the token is clearly being stored but not recognized, it was because the samples.txt file was written using an editor other than the standard unix editors (vim, emacs, nano, etc.) and the fancier editor stored the text with special hidden characters.

If this is the case, try rewriting your samples.txt file using a basic text editor.

best,

~brian

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[LinaYan]

Hello, can you help me please with the same issue? I wrote it in notepad and checked and rewrote in nano, but I get the same error as topicstarter had.

My samples text on screen/

Error I got:

Error, cannot determine column index for replicate name [MC_1b_S7_L001]$VAR1 = {
          'MC_22_1_S9_L002clean' => 11,
          'MC_2_1a_S8_L001clean' => 5,
          'MC_22_1_S9_L001unpaired' => 10,
          'MC_1b_S7_L002clean' => 3,
          'MC_22_1_S9_L001clean' => 9,
          'MC_22_1_S9_L002unpaired' => 12,
          'MC_2_1a_S8_L002unpaired' => 8,
          'MC_2_1a_S8_L002clean' => 7,
          'MC_1b_S7_L002unpaired' => 4,
          'MC_1b_S7_L001_001clean' => 1,
          'MC_2_1a_S8_L001unpaired' => 6,
          'MC_1b_S7_L001_001unpaired' => 2
        };

четверг, 6 июля 2017 г. в 18:44:09 UTC+3, bh...@broadinstitute.org:

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[Brian Haas]

Hi,

It looks like your count matrix file has column names that aren't
consistent with those in your samples.txt file.

For example, it's looking for the column 'MC_1b_S7_L001' but finding
instead 'MC_1b_S7_L001_001unpaired', and it looks like your column
names have clean, paired, unpaired, etc., attached to them.

If you update your count matrix column names, I expect it should work.

~b

On Mon, Nov 28, 2022 at 1:25 PM LinaYan <sonyaint...@gmail.com> wrote:
>
> Hello, can you help me please with the same issue? I wrote it in notepad and checked and rewrote in nano, but I get the same error as topicstarter had.

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