Hi all,
I've done some clustering using Trinity's define_clusters_by_cutting_tree.pl script, and am having a bit of an issue.
The data I'm analysing is from a time series: D1, D2, D3, D4, D6, D8, D10, D12, D14
When I went through the trinity pipeline, the sample order was mixed up in the matrices produced, so I went back and redid it with the names D01, D02, D03, D04, D06, D08, D10, D12, D14
Now the sample order is perfect in the matrices produced, however, the order of samples is still mixed up when I do the cluster analysis using the corrected matrix.
Any way I can do the cluster analysis and have the samples in the correct order? It really doesn't make sense to have day 2 next to day 10 for example... It produces patterns that aren't intuitive....
Cheers,
Kelli