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

Blog Article

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 Dispensers comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes.Based on this transcript-level 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 Solar Power cross-platform concordance.Conclusion We conclude that our transcript-level reannotation and 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.