Biostatistical considerations of the use of genomic DNA reference in microarrays

Yunfeng Yang, Michelle Zhu, Liyou Wu, Jizhong Zhou

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

1 Citation (Scopus)

Abstract

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories (2, 3, 5, 7, 9, 20, 24-26). While some reported that experimental results of microarrays using genomic DNA reference conformed nicely to those obtained by cDNA: cDNA co-hybridization method, others acquired poor results. We hypothesized that these conflicting reports could be resolved by biostatistical analyses. To test it, microarray experiments were performed in a γ-proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either by direct cDNA: cDNA co-hybridization, or by indirect calculation through a Shewanella genomic DNA reference. Several major biostatistical techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses significantly improved the data quality. These findings could potentially serve as guidelines for microarray data analysis using genomic DNA as reference.

Original languageEnglish
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages593-600
Number of pages8
DOIs
StatePublished - 1 Dec 2007
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: 14 Jan 200717 Jan 2007

Publication series

NameProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Other

Other7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period14/01/0717/01/07

Fingerprint

Microarrays
DNA
Complementary DNA
Shewanella
Proteobacteria
Random errors
Microarray Analysis
Experiments
Guidelines

Cite this

Yang, Y., Zhu, M., Wu, L., & Zhou, J. (2007). Biostatistical considerations of the use of genomic DNA reference in microarrays. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE (pp. 593-600). [4375621] (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE). https://doi.org/10.1109/BIBE.2007.4375621
Yang, Yunfeng ; Zhu, Michelle ; Wu, Liyou ; Zhou, Jizhong. / Biostatistical considerations of the use of genomic DNA reference in microarrays. Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. pp. 593-600 (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).
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Yang, Y, Zhu, M, Wu, L & Zhou, J 2007, Biostatistical considerations of the use of genomic DNA reference in microarrays. in Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE., 4375621, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, pp. 593-600, 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE, Boston, MA, United States, 14/01/07. https://doi.org/10.1109/BIBE.2007.4375621

Biostatistical considerations of the use of genomic DNA reference in microarrays. / Yang, Yunfeng; Zhu, Michelle; Wu, Liyou; Zhou, Jizhong.

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 593-600 4375621 (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE).

Research output: Chapter in Book/Report/Conference proceedingConference contributionResearchpeer-review

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Yang Y, Zhu M, Wu L, Zhou J. Biostatistical considerations of the use of genomic DNA reference in microarrays. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. 2007. p. 593-600. 4375621. (Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE). https://doi.org/10.1109/BIBE.2007.4375621