Literature DB >> 19734302

On the causes of outliers in Affymetrix GeneChip data.

Graham J G Upton1, Olivia Sanchez-Graillet, Joanna Rowsell, Jose M Arteaga-Salas, Neil S Graham, Maria A Stalteri, Farhat N Memon, Sean T May, Andrew P Harrison.   

Abstract

We describe various types of outliers seen in Affymetrix GeneChip data. We have been able to utilise the data in the Gene Expression Omnibus to screen GeneChips across a range of scales, from single probes, to spatially adjacent fractions of arrays, to whole arrays, to whole experiments. In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips.

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Year:  2009        PMID： 19734302     DOI： 10.1093/bfgp/elp027

Source DB:  PubMed          Journal:  Brief Funct Genomic Proteomic        ISSN： 1473-9550


  14 in total

1.  Analysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization.

Authors:  Andrey Marakhonov; Nataliya Sadovskaya; Ivan Antonov; Ancha Baranova; Mikhail Skoblov
Journal:  BMC Genomics       Date:  2014-12-19       Impact factor: 3.969

2.  From hybridization theory to microarray data analysis: performance evaluation.

Authors:  Fabrice Berger; Enrico Carlon
Journal:  BMC Bioinformatics       Date:  2011-12-02       Impact factor: 3.169

3.  A Brassica exon array for whole-transcript gene expression profiling.

Authors:  Christopher G Love; Neil S Graham; Seosamh O Lochlainn; Helen C Bowen; Sean T May; Philip J White; Martin R Broadley; John P Hammond; Graham J King
Journal:  PLoS One       Date:  2010-09-16       Impact factor: 3.240

Review 4.  Systematic deciphering of cancer genome networks.

Authors:  Bernard Fendler; Gurinder Atwal
Journal:  Yale J Biol Med       Date:  2012-09-25

5.  AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.

Authors:  Mario Fasold; Hans Binder
Journal:  Bioinformatics       Date:  2012-10-24       Impact factor: 6.937

6.  ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

Authors:  Christopher C Overall; D Andrew Carr; Ehsan S Tabari; Kevin J Thompson; Jennifer W Weller
Journal:  BMC Bioinformatics       Date:  2011-05-06       Impact factor: 3.307

7.  Normalized Affymetrix expression data are biased by G-quadruplex formation.

Authors:  Hugh P Shanahan; Farhat N Memon; Graham J G Upton; Andrew P Harrison
Journal:  Nucleic Acids Res       Date:  2011-12-22       Impact factor: 16.971

Review 8.  Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.

Authors:  Andrew Harrison; Hans Binder; Arnaud Buhot; Conrad J Burden; Enrico Carlon; Cynthia Gibas; Lara J Gamble; Avraham Halperin; Jef Hooyberghs; David P Kreil; Rastislav Levicky; Peter A Noble; Albrecht Ott; B Montgomery Pettitt; Diethard Tautz; Alexander E Pozhitkov
Journal:  Nucleic Acids Res       Date:  2013-01-09       Impact factor: 16.971

9.  Estimating RNA-quality using GeneChip microarrays.

Authors:  Mario Fasold; Hans Binder
Journal:  BMC Genomics       Date:  2012-05-14       Impact factor: 3.969

10.  Correction of spatial bias in oligonucleotide array data.

Authors:  Philippe Serhal; Sébastien Lemieux
Journal:  Adv Bioinformatics       Date:  2013-03-13
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