Don’t scrimp on the analysis of your genechip / microarray experimental results!
Genechip / microarray experiments are now very important and useful tools in biomedical research. Genechips, while decreasing in price as cheaper technology is developed, are still expensive. And in a lot of cases, many samples (i.e. microarrays) must be run to have the statistical power to tease out the differences between experimental groups–in particular when you are dealing with human tissue and biological noise is a significant factor to be dealt with. I know many labs that have spent anywhere from $30,000 to almost $100,000 on running the microarrays–getting only the raw data in return for that sum of money.
However, I also know many who then turn around and try to save money by being cheap on the analysis of that raw data. This is so wrong, in particular if you plan on publishing your microarray data rather than just using it as a screening tool to chase targets. For publishing microarray data, the analysis is what makes or breaks your experiment, since the raw data is uninterpretable. You can save some money by using the most basic tools that are available to find some genes that are differentially expressed, but you will get what you pay for. You’ve already spent so much money on the genechips, go on and spend on the analysis too. Regardless of how complicated and sophisticated an analysis you do, it is highly unlikely that you will spend anywhere near what you spent on your genechips (either through buying analysis software, access to databases for your analysis or hiring trained statisticians to show you the cutting edge methods for microarray analysis and then doing the analysis for you if choose not to do the statistical programming yourself). And at the same time, the more sophisticated your analysis (which will hopefully yield more biological insight), the more impact that your final article will have. Microarray papers continue to be published at all levels–from the big 3 of biological research (ie. the journals Nature, Science and Cell) to the most obscure journals you’ve never heard of. If you don’t believe me that your analysis makes your paper, then look up microarray papers in Nature, Science and Cell and compare them to microarrays in any journal you’ve never heard of.
Yes, yes, I know, money is a real factor for many labs. Avoid the problem of money by discussing with your P.I. or advisor the importance of the analysis before you begin your microarray experiment and plan ahead so you balance the number of genechips you use in order to maximize the analysis you can perform after.
Bottomline: don’t scrimp on your microarray analysis! It will hurt you much more than the cost will hurt.
November 5th, 2008 | Tags: microarray, research tools | Category: md / phd student stuff, phd / graduate student stuff, research | Leave a comment
