Entering edit mode
5.7 years ago
majeedaasim
▴
60
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