Is it possible the remove specific gene clusters that don't meet our criteria from a tree analysis. I could not find such an option.
If that is not possible, is it possible to select the clusters that we do want and load them all into a new array. I was able to save clusters as txt files, but found that the program would only let me load one of those at a time.
The ultimate goal is to remove the gene clusters that aren't expressed the same between specific samples, and then re-perform the analysis. Any help is appreciated.
There are lots of different ways to get MeV to do what you want. Here's a round-about way to get it done.
1.) HCL cluster all genes.
2.) Select a node that you want to remove, right click, and select 'Store Cluster'. This puts the gene set in the cluster repository (list of clusters under the node called Cluster Manager).
3.) Repeat step 2 for all sub-trees you want to exclude.
4.) This will seem strange but select KMC (K-means) from the Cluster analysis area and specify to make "1" cluster. This is just a trick to dump all genes into a cluster object.
5.) Open a view containing the one KMC gene cluster. Right click and select 'Store Cluster'.
6.) Now select the cluster manager node for genes to open the table of gene clusters.
7.) IF you have more than one sub-tree of genes to exclude, select all in the table using Ctrl-left click, then right click and select the menu options 'Cluster Operations->Union'. This will combine all gene lists to exclude.
8.) Now select that cluster that represents all genes to exclude and Ctrl-left click on the one KMC cluster containing all genes. Having these 2 clusters selected, right click and select 'Cluster Operations->XOR' to report on genes that are in one cluster or the other but not in both. This is a way to get a new cluster containing just the genes you want.
9.) Select the new cluster containing all the 'good' genes, right click and do one of two options (or both); 'Save Cluster' this will make a new file with just the genes you want that can be reloaded into MeV in a new session, OR select 'Launch New Session' with will open a new array viewer with your gene set of interest. I think it's good to save the file in addition to opening the new view.