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

Authors
Type
Published Article
Journal
BMC Bioinformatics
1471-2105
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Volume
8
Pages
108–108
Identifiers
PMID: 17394657
Source
Medline
License
Unknown

Abstract

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.

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