Cross Platform Comparison


We have conducted a study to compare the variability in measured gene expression levels associated with three types of microarray platforms. Total RNA samples were obtained from liver tissue of four male mice, two each from inbred strains A/J and C57BL/6J. The same four samples were assayed on Affymetrix Mouse Genome Expression Set 430 GeneChips (MOE430A and MOE430B), spotted cDNA microarrays, and spotted oligonucleotide microarrays using eight arrays of each type.


The linked file below contains the data used in a study comparing three different microarray platforms:

  • Affymetrix GeneChip 430A and 430B
  • Compugen two-color spotted microarrays
  • NIA two-color spotted microarrays

Click here to download the data sets. Detailed analysis information can be found in the paper.


Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G
J Biomol Tech 2004 Dec;15:276-284 [ Full Text ] PMCID: PMC2291701

Saltwater marsh in Acadia National Park