Background: Affymetrix GeneChips are an important tool in many facets of biological research. Recently, notable design changes to the chips have been made. In this study, we use publicly available data from Affymetrix to gauge the performance of three human gene expression arrays: Human Genome U133 Plus 2.0 (U133), Human Exon 1.0 ST (HuEx) and Human Gene 1.0 ST (HuGene).
Results: We studied probe-, exon- and gene-level reproducibility of technical and biological replicates from each of the 3 platforms. The U133 array has larger feature sizes so it is no surprise that probe-level variances are smaller, however the larger number of probes per gene on the HuGene array seems to produce gene-level summaries that have similar variances. The gene-level summaries of the HuEx array are less reproducible than the other two, despite having the largest average number of probes per gene. Greater than 80% of the content on the HuEx arrays is expressed at or near background. Biological variation seems to have a smaller effect on U133 data. Comparing the overlap of differentially expressed genes, we see a high overall concordance among all 3 platforms, with HuEx and HuGene having greater overlap, as expected given their design. We performed an analysis of detection rates and area under ROC curves using an experiment made up of several mixtures of 2 human tissues. Though it appears that the HuEx array has worse performance in terms of detection rates, all arrays have similar ability to separate differentially expressed and non-differentially expressed genes.
Conclusion: Despite noticeable differences in the probe-level reproducibility, gene-level reproducibility and differential expression detection are quite similar across the three platforms. The HuEx array, an all-encompassing array, has the flexibility of measuring all known or predicted exonic content. However, the HuEx array induces poorer reproducibility for genes with fewer exons. The HuGene measures just the well-annotated genome content and appears to perform well. The U133 array, though not able to measure across the full length of a transcript, appears to perform as well as the newer designs on the set of genes common to all 3 platforms.