Question: (Closed) Trinity: Problem in "run_DE_analysis.pl"
0
gravatar for majeedaasim
14 months ago by
majeedaasim40
United States
majeedaasim40 wrote:

I used the trinity scripts for differential gene expression. the command I used is

/path/to/run_DE_analysis.pl --matrix RSEM.gene.counts.matrix \
        --method edgeR \
        --samples_file sample_file_forDE \
        --contrasts contrast_file

following information is given

> Got 4 samples, and got: 5 data fields.
> 
Header: S1  S2  W1  W2
> 
> Next: Tx_sum_Rp1_DN1000_c0_g1  22.75  6.99          0.00     0.00

 

$VAR1 = {
      'W2' => 4,
      'S1' => 1,
      'W1' => 3,
      'S2' => 2
    };

$VAR1 = {
      'W1' => [
                'Winter'
              ],
      'S2' => [
                'Summer'
              ],
      'S1' => [
                'Summer'
              ],
      'W2' => [
                'Winter'
              ],
      'Sample' => [
                    'season'
                  ]
    };

Contrasts to perform are: $VAR1 = [
      [
        'Winter',
        'Summer'
      ]
    ];

And then gives the following error:

Can't use an undefined value as an ARRAY reference at /path/to/run_DE_analysis.pl line 383.

how to fix it?

Edit by @RamRS: Trinity version (inferred from path to the perl script) == 2.5.1-0

dge trinity • 482 views
ADD COMMENTlink modified 14 months ago by RamRS24k • written 14 months ago by majeedaasim40

Hello majeedaasim!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

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Cheers!

ADD REPLYlink written 13 months ago by h.mon27k
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