A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences. The analysis gave rise to a different probe-level visualization method that can highlight probe differences according to transcript specificity.The results highlight the need for detailed probe annotation at the transcriptome level. The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms.Microarrays have become a widely used tool to measure gene expression levels on a genome-wide basis and are available from a number of manufacturers. Each platform incorporates proprietary technology, with differences in probe design, probe bioinformatics, probe creation and deposition, reagents and protocols across platforms introducing variability into expression analysis. A large body of work has studied the reproducibility of microarray data and therefore the interchangeability of commercial platforms. A dialogue over data sets, analysis methods, and concordance measures has evolved, but no clear consensus on the level of agreement or disagreement in expression results has been reached.It is generally understood that differences between platforms exist. The source of contention is the interpretation of the magnitude of these differences. Some conclude from the data that microarray results are sufficiently comparable across platforms [1,2]. Others caution that the technological differences have not yet been sufficiently resolved to combi