Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

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Abstract Background Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes.Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis.Results Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes.Based on this transcript-level Pregnancy Tests annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts.In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization.

We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance.Conclusion We conclude that our transcript-level reannotation and Barista Towel redefinition of probe sets complement the original Affymetrix design.Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement.Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes.For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software.