V2 notes from user testing

This page was intended to capture  "gotchas" and "confusions" that users encountered in using the V2 software. These observations can now be captured in Bugzilla as documentation and/or software enhancements.

CLS file problem

CLS file with four classes which was loadable to GSEA ver1 does not load anymore:

22 4 1
#WTnd WThf KOnd KOhf WTnd WThf KOhf KOhf WTnd WTnd WTnd WTnd WTnd KOnd KOnd KOnd KOnd KOnd KOnd WThf WThf WThf WThf KOhf KOhf KOhf

It loads after changing it to:

22 2 1
#WT KO
WT WT KO KO WT WT WT WT WT KO KO KO KO KO KO WT WT WT WT KO KO KO

darked 13:29, 21 July 2006 (EDT)

==Java Heap Space error===

On a 2GB Windows XP workstation with no other than GSEA applications running I am getting:

java.lang.OutOfMemoryError: Java heap space

using all.may_2006.symbols_mapped_to_Mouse430_2.gmt, CLS mentioned above + expression file (derived from 22 CEL files of Mouse430_2 platform), 100 permutations .

1) Can I somehow increase available memory, i.e. by running it on a command line?

2) Any other ideas how to complete the job?

darked 14:26, 21 July 2006 (EDT)