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Evaluation of the gene-specific dye bias in cDNA microarray experiments

M.-L. Martin-Magniette, J. Aubert, E. Cabannes, J.-J. Daudin
2005 Bioinformatics  
Motivation: In cDNA microarray experiments all samples are labeled with either Cy3 or Cy5. Systematic and gene-specific dye bias effects have been observed in dual-color experiments.  ...  Methods: The gene-specific dye bias is taken into account using an analysis of variance model. We propose an index, named label bias index, to measure the gene-specific dye bias.  ...  Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments' BIOINFORMATICS Fig. 1 . 1 Plots of the log-ratios log 2 (R/G): first slide in x-axis and second slide in y-axis  ... 
doi:10.1093/bioinformatics/bti302 pmid:15691855 fatcat:urbppi65jjftrbuzscw2eeiwwy

Comment on 'Evaluation of the gene-specific dye bias in cDNA microarray experiments'

K. K. Dobbin, J. H. Shih, R. M. Simon
2005 Bioinformatics  
For example, in an experiment to evaluate the effect of different conditions on cell line gene expression, one must perform independent replicates of the experiment, in which multiple, different cell line  ...  The specific model equation 2 for the log-ratios is where Z ig is the normalized log-ratio for gene g on array i, (VG) 1g − (VG) 2g is the 'variety' effect, (DG) 1g − (DG) 2g is genespecific dye bias and  ...  For example, in an experiment to evaluate the effect of different conditions on cell line gene expression, one must perform independent replicates of the experiment, in which multiple, different cell line  ... 
doi:10.1093/bioinformatics/bti428 pmid:15817695 fatcat:bnwv6dvjhnfdzcygdxfstfxyzi

Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'

M.-L. Martin-Magniette, J. Aubert, E. Cabannes, J.-J. Daudin
2005 Bioinformatics  
We, however, want to make it clear that our manuscript primarily focuses on the detection, quantification and correction of the gene-specific dye-bias introduced in dual-color microarray experiments.  ...  Their remarks relate to the design of microarray experiments and notably about the use of dye-swaps.  ... 
doi:10.1093/bioinformatics/bti479 pmid:15941744 fatcat:ojwvu2ykonaztptovfe46nwya4

Dye bias correction in dual-labeled cDNA microarray gene expression measurements

Barry A Rosenzweig, P Scott Pine, Olen E Domon, Suzanne M Morris, James J Chen, Frank D Sistare
2004 Environmental Health Perspectives  
A significant limitation to the analytical accuracy and precision of dual-labeled spotted cDNA microarrays is the signal error due to dye bias.  ...  Incorporating split-control microarrays within a set of concurrently processed hybridizations to specifically measure dye bias can eliminate the need for technical dye swap replicates and reduce microarray  ...  It is unclear whether small changes in such protocols could further minimize or even worsen dye bias with the specific cDNA microarray used in these experiments.  ... 
doi:10.1289/ehp.6694 pmid:15033598 pmcid:PMC1241902 fatcat:l5jcosndcbdvlmg6n3ogsbvhxi

Improvement of condition for hybridization to obtain high sensitivity in oligonucleotide microarray systems

Wataru GUNJI, Takahito KAI, Takahiko UTSUGI, Fumitoshi ONODA, Yasufumi MURAKAMI
2005 JSM Mycotoxins  
The rotary hybridization reduces uniformity of hybridization efficiency and results in the reduction of the fluorescent dye bias caused by the different amount of hybridized probe between differently labeled  ...  The DNA microarray technology is a very useful tool for a comprehensive analysis of the gene expression profile.  ...  in dye incorporation, and the amplification bias and so on.  ... 
doi:10.2520/myco.55.117 fatcat:p5ktevwlirdptmzw3x7g6pdoqm

Normalization of microarray data: single-labeled and dual-labeled arrays

Jin Hwan Do, Dong-Kug Choi
2006 Molecules and Cells  
Various computational tools have been created to facilitate the analysis of the large volume of data produced in DNA microarray experiments.  ...  Therefore, the knowledge of underlying assumption and principle of normalization would be helpful for the correct analysis of microarray data.  ...  The third type of dye bias indicates the dependency on some subset of genes, and called gene-specific bias.  ... 
pmid:17202852 fatcat:esn7sk2665awtguwrnwjpmdyha

Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays

Marcel von der Haar, Christopher Heuer, Martin Pähler, Kathrin von der Haar, Patrick Lindner, Thomas Scheper, Frank Stahl
2016 Biology  
These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.  ...  The model efficiently normalizes the bias introduced by this effect with respect to the choice of dye, the previously carried out scans, and the scanner settings [19] .  ...  Regarding FRET, the same parameters used to evaluate this effect in the 96 gene experiment do not yield the expected results in the 24 gene experiment.  ... 
doi:10.3390/biology5040047 pmid:27916881 pmcid:PMC5192427 fatcat:7cfq2yw5evgohlcbsnryetz67i

Design issues in toxicogenomics using DNA microarray experiment

K LEE, J KIM, D KANG
2005 Toxicology and Applied Pharmacology  
Biases in subject selection and exposure assessment should be minimized, and confounding bias should also be controlled for in stratified or multiple regression analysis.  ...  In omics study, microarray is the most popular approach.  ...  Sample size A number of population studies were conducted to evaluate the effect of genetic variant on specific diseases.  ... 
doi:10.1016/j.taap.2005.01.045 pmid:16005921 fatcat:uhi7ndzxpnhipmstm7j3ylf5ea

Experimental Design and Analysis of Antibody Microarrays: Applying Methods from cDNA Arrays

Jeanette E. Eckel-Passow, Antje Hoering, Terry M. Therneau, Irene Ghobrial
2005 Cancer Research  
As is also the case with gene expression microarrays, it is hoped that protein expression microarrays will aid in biomarker discovery, predicting disease outcomes and response to treatments, and detecting  ...  In the last five years, a large amount of research has been devoted to twocolor cDNA arrays to improve experimental design, normalization and statistical analyses to assess differential expression and  ...  The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C.  ... 
doi:10.1158/0008-5472.can-04-3213 pmid:15833819 fatcat:37b25thcgjckrikgdcxm4nnugy

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David D L Bowtell, Gordon K Smyth
2006 BMC Bioinformatics  
The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model.  ...  A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays.  ...  Acknowledgements The authors are grateful for discussions with Terry Speed. AO and GKS were supported by Australian NHMRC Project Grant 257259 and Program Grant 406657.  ... 
doi:10.1186/1471-2105-7-511 pmid:17118209 pmcid:PMC1664592 fatcat:nwqdxtcyzjfkhht7qmese3pota

Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data

Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau, Xuhua Xia
2008 BMC Bioinformatics  
Normalization is essential in dual-labelled microarray data analysis to remove nonbiological variations and systematic biases.  ...  However, all these popular approaches have critical assumptions about data distribution, which is often not valid in practice.  ...  Dabrowski (Dept. of Mathematics, University of Ottawa), who passed away on October 7, 2006. He was keenly interested in microarray data normalization.  ... 
doi:10.1186/1471-2105-9-25 pmid:18199333 pmcid:PMC2275243 fatcat:l4lov2ph5bcztpx2r4dh43ayr4

A rapid and inexpensive labeling method for microarray gene expression analysis

Mario Ouellet, Paul D Adams, Jay D Keasling, Aindrila Mukhopadhyay
2009 BMC Biotechnology  
However, the simplicity and cost-effectiveness of the new method allows for increased sample throughput in microarray experiments and makes the process amenable to automation with a relatively simple liquid  ...  Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray  ...  Acknowledgements This work was part of the DOE Joint BioEnergy Institute http:// www.jbei.org supported by the U. S.  ... 
doi:10.1186/1472-6750-9-97 pmid:19939278 pmcid:PMC2790446 fatcat:w46vhaveevavnndszdbehsstsy

Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays

Xujing Wang, Shuang Jia, Lisa Meyer, Bixia Xiang, Li-Yen Chen, Nan Jiang, Carol Moreno, Howard J Jacob, Soumitra Ghosh, Martin J Hessner
2006 BMC Bioinformatics  
With that highly accurate gene expression measurements can be achieved using the cDNA microarray technology.  ...  We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities  ...  We thank Rhonda Geoffrey, Sanaa Muheisen for assisting the data preparation, and Pawjai Khampang for careful reading of the manuscript.  ... 
doi:10.1186/1471-2105-7-378 pmid:16907976 pmcid:PMC1563483 fatcat:mscmy256urgg5h2hx3y5ub4jta

Page 1999 of Genetics Vol. 172, Issue 3 [page]

2006 Genetics  
Simon, 2005a Comment on ‘Eval- uation of the gene-specific dye bias in cDNA microarray experi- ments.’ Bioinformatics 21: 2803-2804. Dossin, K. K., E. S. Kawasaki, D. W. PETERSEN and R. M.  ...  Simon, 2005b Characterizing dye bias in microarray experiments. Bio- informatics 21: 2430-2437. HuBner, N., C. A. WALLACE, H. ZimpAHL, E. PETRETTO, H.  ... 

Comparison of two probe preparation methods using long oligonucleotide microarrays

Fahd Al-Mulla, Raba' Al-Tamimi, Milad S. Bitar
2004 BioTechniques  
The use of oligonucleotides as a capture platform for microarray-based experiments is gaining popularity.  ...  A confirmatory step involving real-time reverse transcription PCR (RT-PCR) of 18 selected genes favors the superiority of the cDNA fluorescent labeling over the T7 labeling method.  ...  This work was funded in part by grant no. 99-07-07 from the Kuwait Foundation for the Advancement of Sciences and the Graduate College of Kuwait University.  ... 
doi:10.2144/04375rr03 pmid:15560138 fatcat:lon77yl5uzbqzmi4oj244nulae
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