Choosing a Study Platform
The choice of microarray platform, like the choice of study organism, depends on a number of factors and does not really have a "right" answer. Here, we present some guidelines to help investigators make their decision.
- Study Organism: Mouse and Human arrays are available on every platform, and most platforms have a Rat array. With any other organism, however, you will most likely need to use Affymetrix or a custom array
- Genes of Interest: Most of the arrays available are designated "whole genome", and so there is considerable overlap in the genes queried. There are differences between the platforms, however, and we strongly recommend that investigators check that the platform they are considering carries their gene(s) of interest. A good starting point for this query is the VMSR Cross-Platform Search
- Cost: When cost is the limiting factor in the decision-making process, most investigators choose the spotted arrays. Contact the VMSR for full pricing information
- Experimental Groups: If you are trying to compare three or more experimental groups, two-color microarrays become quite cumbersome. With two-color arrays, you would either need to hybridize all possible pairs of samples, or make indirect comparisons. With experiments of this type, we strongly recommend a one-color array
- Sample Abundance: While we offer RNA Amplification services for most of our microarray platforms, we recommend that amplification be avoided if at all possible. If you have difficulty obtaining more than a microgram or two of total RNA from your samples, we urge you to consider a commercial array - starting requirements tend to be lower, and one-color arrays usually require less sample over the course of the experiment
- Collaboration: If you will be comparing your data with someone else's microarray data, you should consider the platform they are using. While we are comfortable with the coverage and quality of all of our platforms, Affymetrix is the most popular microarray around the world
- Prior Experience: Some labs have used a particular technology in the past and are comfortable with it. While this should never be the entire basis of your decision, it is something to consider when all else is equal
