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.
I've tried the trial version of Genespring and practically everything you can do in Genespring you can do in Bioconductor (http://www.bioconductor.org/), which is open source and free! Of course, if you want to use Bioconductor, you will have to learn how to work in R-language, and it's not all nice and point-and-click (command line), but if you have someone who is willing to dive into R-language, this person will learn a lot about statistics along the way, plus you can completely customize the way you analyze the data.
ReplyDeleteUnfortunately the reason we're using GeneSpring isn't its power but its ease of use. We don't want to learn R or a lot of powerful statistics, and we very much do want to just point and click.
ReplyDeleteI think somewhere I have a post explaining that we're generalists, needing to do a lot of things with only modest expertise, rather than specialists who can invest the time to learn a few things very well.
I sympathize, Rosie. And can't offer much help, except I know some very happy GeneSpring users, so perhaps the investment of time, money and energy will feel worthwhile in the long run.
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