A comparison of Affymetrix gene expression arrays

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Affymetrix GeneChips are crucial tools in biological research.
• Recent design changes necessitate performance evaluation of human gene expression arrays.

Purpose of the Study:

• To assess and compare the performance of three Affymetrix human gene expression arrays: Human Genome U133 Plus 2.0 (U133), Human Exon 1.0 ST (HuEx), and Human Gene 1.0 ST (HuGene).

Main Methods:

• Analysis of probe-, exon-, and gene-level reproducibility using technical and biological replicates.
• Evaluation of detection rates and ROC curves using mixed human tissue samples.
• Comparison of gene expression data across the three array platforms.

Main Results:

• The U133 array shows smaller probe-level variances due to larger feature sizes.
• HuGene arrays provide gene-level summaries with variances similar to U133, despite more probes.
• HuEx arrays exhibit lower gene-level reproducibility and high background expression; U133 data is less affected by biological variation.
• All arrays demonstrate high concordance in detecting differentially expressed genes, with HuEx and HuGene showing greater overlap.

Conclusions:

• Gene-level reproducibility and differential expression detection are comparable across U133, HuEx, and HuGene arrays, despite probe-level variations.
• HuEx arrays offer broad exonic content measurement but show poorer reproducibility for genes with fewer exons.
• HuGene arrays perform well, focusing on well-annotated genomic content.
• The U133 array performs comparably to newer designs for commonly measured genes, despite not measuring full transcript lengths.