Assessing probe-specific dye and slide biases in two-color microarray data

Ruixiao Lu; Geun-Cheol Lee; Shultz, Michael; Dardick, Chris; Kihong Jung; Phetsom, Jirapa; Yi Jia; Rice, Robert H.; Goldberg, Zelanna; Schnable, Patrick S.; Ronald, Pamela; Rocke, David M.
January 2008
BMC Bioinformatics;2008, Vol. 9, Special section p1
Academic Journal
Background: A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any differences between the dyes can be adjusted out by standard methods of normalization, so that measures such as log ratios on the same slide are reliable measures of comparative expression. However, even after the normalization, there are still probe specific dye and slide variation among the data. We define a method to quantify the amount of the dye-by-probe and slide-by-probe interaction. This serves as a diagnostic, both visual and numeric, of the existence of probe-specific dye bias. We show how this improved the performance of two-color array analysis for arrays for genomic analysis of biological samples ranging from rice to human tissue. Results: We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function), though numerical results are also obtained. Conclusion: We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor.


Related Articles

  • Relationship between gene co-expression and probe localization on microarray slides. Kluger, Yuval; Haiyuan Yu; Jiang Qian; Gerstein, Mark // BMC Genomics;2003, Vol. 4, p49 

    Background: Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes. Results: In this work we...

  • MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. Honore, Paul; Granjeaud, Samuel; Tagett, Rebecca; Deraco, Stephane; Beaudoing, Emmanuel; Rougemont, Jacques; Debono, Stephane; Hingamp, Pascal // BMC Genomics;2006, Vol. 7, p240 

    Background: High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP...

  • DNA Microarrays in Clinical Cancer Research. Wadlow, Raymond; Ramaswamy, Sridhar // Current Molecular Medicine;Feb2005, Vol. 5 Issue 1, p111 

    The recent sequencing of the human genome, coupled with advances in biotechnology, is enabling the comprehensive molecular “profiling” of human tissues. In particular, DNA microarrays are powerful tools for obtaining global views of human tumor gene expression. Complex information...

  • Construction and characterization of normalized cDNA library of maize inbred MO17 from multiple tissues and developmental stages. Zhang, Z. X.; Zhang, F. D.; Tang, W. H.; Pi, Y. J.; Zheng, Y. L. // Molecular Biology;Mar2005, Vol. 39 Issue 2, p177 

    A comprehensive complementary DNA (cDNA) library is a valuable resource for functional genomics. In this study, we set up a normalized cDNA library of Mo17 (MONL) by saturation hybridization with genomic DNA, which contained expressed genes of eight tissues and organs from inbred Mo17 of maize...

  • "Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays. Kanno, Jun; Aisaki, Ken-ichi; Igarashi, Katsuhide; Nakatsu, Noriyuki; Ono, Atsushi; Kodama, Yukio; Nagao, Taku // BMC Genomics;2006, Vol. 7, p64 

    Background: Transcriptome data from quantitative PCR (Q-PCR) and DNA microarrays are typically obtained from a fixed amount of RNA collected per sample. Therefore, variations in tissue cellularity and RNA yield across samples in an experimental series compromise accurate determination of the...

  • MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. Henckel, Kolja; Küster, Helge; J.^Stutz, Leonhard; Goesmann, Alexander // BMC Research Notes;2010, Vol. 3, p262 

    Background: Expressed Sequence Tags (ESTs) are in general used to gain a first insight into gene activities from a species of interest. Subsequently, and typically based on a combination of EST and genome sequences, microarraybased expression analyses are performed for a variety of conditions....

  • Characterization of a newly developed chicken 44K Agilent microarray. Xianyao Li; Hsin-I Chiang; Zhu, James; Dowd, Scot E.; Huaijun Zhou // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: The development of microarray technology has greatly enhanced our ability to evaluate gene expression. In theory, the expression of all genes in a given organism can be monitored simultaneously. Sequencing of the chicken genome has provided the crucial information for the design of a...

  • SNPinProbe_l.0: A database for filtering out probes in the Affymetrix GeneChip Human Exon 1.0 ST array potentially affected by SNPs. Shiwei Duan; Wei Zhang; Bleibel, Wasim Kamel; Cox, Nancy Jean; Dolan, M. Eileen // Bioinformation;2008, Vol. 2 Issue 10, p469 

    The Affymetrix GeneChip® Human Exon 1.0 ST array (exon array) is designed to measure both gene-level and exon-level expression in human samples. This exon array contains ~1.4 million probesets consisting of ~5.4 million probes and profiles over 17,000 well-annotated gene transcripts in the...

  • A weighted average difference method for detecting differentially expressed genes from microarray data. Kadota, Koji; KNakai, Yuji; KShimizu, Kentaro // Algorithms for Molecular Biology;2008, Vol. 3, Special section p1 

    Background: Identification of differentially expressed genes (DEGs) under different experimental conditions is an important task in many microarray studies. However, choosing which method use for a particular application is problematic because its performance depends on the evaluation metric,...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics