We did fork out the $$$$ for GeneSpring to analyze our new microarray data, and the post-docs have been hard at work analyzing their E. coli Sxy arrays. It looks like E. coli Sxy and H. influenzae Sxy have overlapping but not identical effects.
It's not clear yet whether these differences are in quality or in kind. That is, using a cutoff of at least a 4-fold effect in at least 3 of the 4 replicate arrays, some genes are turned on (or off) by E. coli Sxy but not by H. influenzae Sxy. But in some cases it may just be that these genes are affected more strongly by E. coli Sxy than by H. influenzae Sxy.
The postdocs have also had to work hard to get GeneSpring set up. The promised 24/7 tech support appears to have been outsourced, with phone advisors who rely on a set of help files rather than personal experience. Some of its promised functionalities can't be made to work at all, even with the data that comes with the software. We've escalated our complaints, and results are promised, but of course not until after the holidays.
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