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Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays

Roman Jaksik, Michal Marczyk, Joanna Polanska, Joanna Rzeszowska-Wolny
2013 Sensors  
In this work we present the influence of probe-related design variations on the expression intensities of individual probes, focusing on five potential sources of high probe signal variance: the GC composition  ...  Despite huge advances in the field of microarray probe design methods, the signal variation between probes that target a single transcript is substantially larger than their between-replicate array variability  ...  Acknowledgments We thank Ronald Hancock for critical reading of the manuscript and Anna Lalik, Robert Herok for helpful discusions regarding microarray experiments.  ... 
doi:10.3390/s140100532 pmid:24385030 pmcid:PMC3926573 fatcat:iqbulq524rg7blrxz5uxyjsfqa

Reliability and reproducibility issues in DNA microarray measurements

S DRAGHICI, P KHATRI, A EKLUND, Z SZALLASI
2006 Trends in Genetics  
The main problems seem to be the sub-optimal design or choice of probes and some incorrect probe annotations. Welldesigned data-analysis approaches can rectify some of these problems.  ...  DNA microarrays enable researchers to monitor the expression of thousands of genes simultaneously. However, the current technology has several limitations.  ...  This might explain some of the discrepancies often observed between cDNA and short oligonucleotide microarrays.  ... 
doi:10.1016/j.tig.2005.12.005 pmid:16380191 pmcid:PMC2386979 fatcat:7hhjcmjl4nfe7foc7j5335awga

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases

Leo Lahti, Aurora Torrente, Laura L. Elo, Alvis Brazma, Johan Rung
2013 Nucleic Acids Research  
While short oligonucleotide arrays constitute a major source of genome-wide profiling data, scalable probe-level preprocessing algorithms have been available only for few measurement platforms based on  ...  Unlike the alternatives, the proposed algorithm scales up in linear time with respect to sample size and is readily applicable to all short oligonucleotide platforms.  ...  Incorporating prior information of the probes Estimation of the probe-specific variance parameters is based on probe-level differential expression signal s tj À s rj between each sample t ¼ ½1, . . .  ... 
doi:10.1093/nar/gkt229 pmid:23563154 pmcid:PMC3664815 fatcat:7ylipm7bljhepbydebdi7wvbxy

Tutorial section: There is no silver bullet -- a guide to low-level data transforms and normalisation methods for microarray data

D. P. Kreil
2005 Briefings in Bioinformatics  
In this tutorial paper we review the problem and a selection of solutions, explaining the basic principles behind normalisation procedures and providing guidance for their application.  ...  microarrays have to be combined.  ...  Platforms can be categorised by their probe type. There are three distinct types of microarray probes -cDNA probes, long oligonucleotide probes and short oligonucleotide probes.  ... 
doi:10.1093/bib/6.1.86 pmid:15826359 fatcat:bciww2gfsbcsxocbbqrsg2czfm

Long oligonucleotide microarrays for African green monkey gene expression profile analysis

Béatrice Jacquelin, Véronique Mayau, Guillaume Brysbaert, Béatrice Regnault, Ousmane M. Diop, Fernando Arenzana-Seisdedos, Lars Rogge, Jean-Yves Coppée, Françoise Barré-Sinoussi, Arndt Benecke, Michaela C. Müller-Trutwin
2007 The FASEB Journal  
We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes) and short oligonucleotide arrays (25mer).  ...  The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A-activated CD4 ؉ T cells vs. nonactivated T cells of two monkey  ...  National de la Recherche Scientifique (CNRS), the Région Nord, and the French Ministry of Research through the "Complexité du Vivant Action STICS-Santé" program.  ... 
doi:10.1096/fj.07-8271com pmid:17507667 fatcat:mdkck525zrfyrelpekputfoxua

Review of the literature examining the correlation among DNA microarray technologies

Carole L. Yauk, M. Lynn Berndt
2007 Environmental and Molecular Mutagenesis  
DNA microarray technologies are used in a variety of biological disciplines.  ...  We suggest several key factors that should be controlled in comparing across technologies, and are good microarray practice in general. Environ. Mol. Mutagen. 48:380-394, 2007.  ...  these sources for a more in-depth overview of microarray technologies.  ... 
doi:10.1002/em.20290 pmid:17370338 pmcid:PMC2682332 fatcat:kwa5kp26sbhqdgza26s5jzybmq

Analysis of matched mRNA measurements from two different microarray technologies

W. P. Kuo, T.-K. Jenssen, A. J. Butte, L. Ohno-Machado, I. S. Kohane
2002 Bioinformatics  
calculating correlation between matched measurements and calculating concordance between cluster from two high-throughput DNA microarray technologies, Stanford type cDNA microarrays and Affymetrix oligonucleotide  ...  This suggest gene-specific, or more correctly probe-specific, factors influencing measurements differently in the two platforms, implying a poor prognosis for a broad utilization of gene expression measurements  ...  Acknowledgements This research was supported in part by the grant ''Research Training in Health Informatics'' by the National Library of Medicine, 5T15 LM07092-07.  ... 
doi:10.1093/bioinformatics/18.3.405 pmid:11934739 fatcat:rtngqqayz5hpxovvbv4qiaoffy

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

Steven P Wilder, Pamela J Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Gauguier
2009 BMC Genomics  
In both species, when choosing optimal methods, the agreement between data generated on the Affymetrix and Illumina was excellent; this was verified using qRT-PCR on a selection of genes present on all  ...  The choice of Affymetrix signal extraction technique was shown to have the greatest effect on the concordance across platforms.  ...  On Affymetrix arrays, genes are represented by one or more probe sets, which are short oligonucleotides (25 base pairs) covering distinct sections of the gene synthesised in place through photolithography  ... 
doi:10.1186/1471-2164-10-63 pmid:19196459 pmcid:PMC2652496 fatcat:3avhcqfmhre5znpw46jdjyscfq

Genetic diversity contribution to errors in short oligonucleotide microarray analysis

Matias Kirst, Rico Caldo, Paula Casati, Gene Tanimoto, Virginia Walbot, Roger P. Wise, Edward S. Buckler
2006 Plant Biotechnology Journal  
DNA arrays based on short oligonucleotide ( ≤ 25-mer) probes are being developed for many species, and are being applied to quantify transcript abundance variation in species with high genetic diversity  ...  Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases.  ...  Introduction High-throughput DNA arrays produced by in situ synthesis of short ( ≤ 25-mer) oligonucleotide sequences (Affymetrix, Santa Clara, CA, USA) are one of the most popular platforms for massive  ... 
doi:10.1111/j.1467-7652.2006.00198.x pmid:17309725 fatcat:jax4jeuhmvezdm5oqt5qkosfsy

Patient-based cross-platform comparison of oligonucleotide microarray expression profiles

Joerg Schlingemann, Negusse Habtemichael, Carina Ittrich, Grischa Toedt, Heidi Kramer, Markus Hambek, Rainald Knecht, Peter Lichter, Roland Stauber, Meinhard Hahn
2005 Laboratory Investigation  
In conclusion, similar profiles of relative gene expression were obtained using arrays of either single 70-mer or multiple short 25-mer oligonucleotide probes per gene.  ...  To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes  ...  Acknowledgements We thank Axel Benner for helpful discussions and critical reading of the manuscript as well as Bernd Groner for excellent support.  ... 
doi:10.1038/labinvest.3700293 pmid:16205657 fatcat:shrtsevddvdnjczdmbxqap3yky

Microarray Probe Expression Measures, Data Normalization and Statistical Validation

Silvia Saviozzi, Raffaele A. Calogero
2003 Comparative and Functional Genomics  
Microarray technology is based on deposition/synthesis, in an ordered manner, on a solid surface, of thousands of EST sequences/genes/oligonucleotides.  ...  Due to the high number of generated datapoints, computational tools are essential in microarray data analysis and mining to grasp knowledge from experimental results.  ...  Acknowledgements This work was partially supported by PRIN2001 2001057147 and FIRB RBAU01JTHS grants from the Italian Ministry of University and S&T Research (MIUR).  ... 
doi:10.1002/cfg.312 pmid:18629084 pmcid:PMC2447370 fatcat:mdkaw6l4mbfh3ilbwlmwlznfua

Three microarray platforms: an analysis of their concordance in profiling gene expression

David Petersen, G V R Chandramouli, Joel Geoghegan, Joanne Hilburn, Jonathon Paarlberg, Chang Hee Kim, David Munroe, Lisa Gangi, Jing Han, Raj Puri, Lou Staudt, John Weinstein (+3 others)
2005 BMC Genomics  
Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length).  ...  The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date, but long oligonucleotide platforms are gaining in popularity and will probably replace cDNA arrays.  ...  Ting Qiu and Inna Dzekunova (Advanced Technology Institute/National Cancer Institute) for conducting some of the preliminary microarray experiments with the three platforms.  ... 
doi:10.1186/1471-2164-6-63 pmid:15876355 pmcid:PMC1140753 fatcat:sp5zwczsajh7pkxn23fyesg2aq

Assessment of the swine protein-annotated oligonucleotide microarray

J. P. Steibel, M. Wysocki, J. K. Lunney, A. M. Ramos, Z.-L. Hu, M. F. Rothschild, C. W. Ernst
2009 Animal Genetics  
The specificity and utility of the swine protein-annotated oligonucleotide microarray, or Pigoligoarray (http://www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from  ...  Simple descriptive diagnostic analyses of PM/ MM probe sets are introduced in this paper as useful tools for detecting non-specific hybridization.  ...  Christine Elsik for their roles in development of the Swine Protein-Annotated Oligonucleotide Microarray.  ... 
doi:10.1111/j.1365-2052.2009.01928.x pmid:19515086 fatcat:r4ekas64qnaoxi53kbmpl46grm

Review Article: Current Knowledge on Microarray Technology - An Overview

CN Naidu, Y Suneetha
2012 Tropical Journal of Pharmaceutical Research  
In the field of transcriptomics, the emergence of microarray-based technologies and the design of DNA biochips allow high-throughput studies of RNA expression in cell and tissue at a given moment.  ...  From its emergence to date, several database, software and technology updates have been developed in the field of microarray technology.  ...  Oligonucleotide arrays contain short fragments of DNA (25 base pairs). One of the commercially available oligonucleotide microarrays are the Gene Chips developed by firms such as Affymetrix.  ... 
doi:10.4314/tjpr.v11i1.20 fatcat:mmcib73d3jb2flm4fx4lqhcq2a

Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations

Richard Shippy, Timothy J Sendera, Randall Lockner, Chockalingam Palaniappan, Tamma Kaysser-Kranich, George Watts, John Alsobrook
2004 BMC Genomics  
In all, this study represents the most comprehensive and specifically designed comparison of short-oligonucleotide microarray platforms to date using the largest set of overlapping genes.  ...  There is a considerable amount of interest in correlating results obtained between different microarray platforms.  ...  Acknowledgements Affymetrix GeneChip analyses were performed by the Genomics Shared Service at the Arizona Cancer Center, supported by grant CA23074.  ... 
doi:10.1186/1471-2164-5-61 pmid:15345031 pmcid:PMC517929 fatcat:z6qhqvtzz5fi5bowk3dzzs5kt4
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