Problem: I want to display things that are similar by Genename. This fucntion is present in your program when you select genes that have the same annotation(Analysis->Find...) , and then show a summary of these genes (Analysis->Summary Window...). Is there any way to save an image from the summary window?
Solution: There may be a way in the future to directly export from the summary window. However, in the meantime you can export data for the selected genes to form a valid CDT file, which can then be opened with Java Treeview and used to form images, etc.
First, Select the genes using the annotation search as you described. Then, use Export->Data... to export the data just for the selected genes. If you accept all the defaults, it will make a well-formed CDT file that you can then reopen and export to an image.
If you output a giant Postscript file and then try to open with adobe illustrator and get the error "The MPS parser is unable to parse the file" it most likely means that the postscript file created by java treeview requires a bigger canvas to display than the maximum canvas size of illustrator. I don't have a good answer on how to fix this, other than lowering the xscale and yscale.
Symptom: Trying to export some big clusters with names and dendogram to GIF, but continually getting an 'Out of memory' error. Able to export results only if you scale down the cluster image (i.e. using low X & Y scale values).
Solution: The gif encoder in java treeview sucks. Use Export->Export to bitmap... (ppm) format and then convert to gif with some software with a better gif encoder. "GraphicConverter" which comes by default with Mac OS X works well. There are also various windows options, such as "Image Transformer", which is shareware.
Note- this section is deprecated, as the GIF encoder is no longer used.