Hi,

I get the following error when trying to do a DE analysis

/trinityrnaseq_r20140413/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix Trinity_trans.TMM.fpkm.matrix -P 1e-3 -C 2
Error, not finding replicates corresponding to cond: RSEM.  Please use the --samples parameter to specify sample/replicate relationships

$VAR1 = {
          'leaf.RSEM' => [
                           'leaf.RSEM'
                         ],
          'leaf_trichome.RSEM' => [
                                    'leaf_trichome.RSEM'
                                  ],
          'root.RSEM' => [
                           'root.RSEM'
                         ],
          'trichome.RSEM' => [
                               'trichome.RSEM'
                             ]
        };

Please let me know how to solve this. What should be the sample file format?

Regards

Vishwesh