Salvaging Affymetrix probes after probe-level re-annotation.

BMC Research Notes
Wim C de LeeuwTimo M Breit

Abstract

Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This results in custom Chip Description Files (CDF). Using these custom CDFs improves the quality of the data and thus the results of related gene expression studies. However, 44-71% of the probes on a GeneChip are lost in this re-annotation process. Although generally aimed at less known genes, losing these probes obviously means a substantial loss of expensive experiment data. Biologists are therefore very reluctant to adopt this approach. We aimed to re-introduce the non-affected Affymetrix probe-sets after these re-annotation procedures. For this, we developed an algorithm (CDF-Merger) and applied it to standard Affymetrix CDFs and custom Brainarray CDFs to obtain Hybrid CDFs. Thus, salvaging lost Affymetrix probes with our CDF-Merger restored probe content up to 94%. Because the salvaged probes (up to 54% of the probe content on the arrays) represent less-reliable probe-sets, we made the origin of all probe-set definitions traceable, so biologists can choose at any time in their analyses, which subset of probe-sets they wan...Continue Reading

References

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Citations

Mar 24, 2012·Animal : an International Journal of Animal Bioscience·N MachM A Smits
Jan 3, 2012·Nucleic Acids Research·Stephanie SchneiderUlla Hansen
Apr 28, 2010·Toxicological Sciences : an Official Journal of the Society of Toxicology·Dorien A M van DartelAldert H Piersma
Sep 25, 2010·Toxicological Sciences : an Official Journal of the Society of Toxicology·Joshua F RobinsonAldert H Piersma
May 27, 2011·Toxicological Sciences : an Official Journal of the Society of Toxicology·Peter T TheunissenAldert H Piersma
Jul 1, 2011·Toxicological Sciences : an Official Journal of the Society of Toxicology·Petra C E van KesterenMirjam Luijten
Nov 3, 2011·Toxicological Sciences : an Official Journal of the Society of Toxicology·Peter T TheunissenAldert H Piersma
Dec 18, 2012·Toxicological Sciences : an Official Journal of the Society of Toxicology·Peter T TheunissenAldert H Piersma
Dec 6, 2011·BMC Bioinformatics·Fabrice Berger, Enrico Carlon
Jun 20, 2012·Archives of Toxicology·Mirjam M SchaapMirjam Luijten
Oct 2, 2014·Archives of Toxicology·Mirjam M SchaapMirjam Luijten
Nov 10, 2010·Journal of Applied Toxicology : JAT·Xiaolian YuanMirjam Luijten
Nov 2, 2016·BMC Genomics·Conrad Droste, Javier De Las Rivas
May 14, 2014·Archives of Toxicology·Kirsten C G Van DyckeGijsbertus T J van der Horst
Sep 25, 2017·F1000Research·Zhaleh SafikhaniBenjamin Haibe-Kains

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Methods Mentioned

BETA
Chip

Software Mentioned

Brainarray
AffyProbeMiner
R
Affymetrix
BioConductor affy library
Affymetrix NetAffx
GeneAnnot
ADAPT
Hybrid CDF R
Ensembl

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