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.

1. Study Organism: The Applied Biosystems and Illumina platforms have whole genome arrays for Human, Mouse and Rat. With any other organism, however, you will most likely need to use Affymetrix or a custom array (http://microarray.emory.edu)
2. 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.
3. Sample Abundance: While we offer RNA Amplification services starting with as little as 50 ng of RNA, 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 all of your samples, we urge you to plan on amplifying ALL of your samples, since it is not recommended to compare amplified and unamplified samples.
4. Collaboration: If you will be comparing your data with someone else's microarray data, you should consider the platform they are using. While cross-platform comparisons of microarray data are possible, they are cumbersome and require separate analyses of each dataset.
5. Data Analysis: One of the strengths of the Applied Biosystems Platform is the ease of data analysis. The platform uses a single 60-mer oligonucleotide probe for each gene. Extensive annotation and analysis tools are available at pantherDB website. The Illumina platform uses a single 50-mer oligonucleotide probe for each gene. Initial data analysis is done in the BeadStudio software from Illumina and can be exported from there for analysis in virtually any other analysis software.