Analysis of Repeatability in Spotted CDNA Microarrays

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2002 Jul 24

PMID 12136105

Citations 18

Authors

Tor-Kristian Jenssen

Mette Langaas

Winston P Kuo

Birgitte Smith-Sorensen

Ola Myklebost

Eivind Hovig

Affiliations

Soon will be listed here.

Abstract

We report a strategy for analysis of data quality in cDNA microarrays based on the repeatability of repeatedly spotted clones. We describe how repeatability can be used to control data quality by developing adaptive filtering criteria for microarray data containing clones spotted in multiple spots. We have applied the method on five publicly available cDNA microarray data sets and one previously unpublished data set from our own laboratory. The results demonstrate the feasibility of the approach as a foundation for data filtering, and indicate a high degree of variation in data quality, both across the data sets and between arrays within data sets.

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Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.

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Characterisation and correction of signal fluctuations in successive acquisitions of microarray images.

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Assessing and selecting gene expression signals based upon the quality of the measured dynamics.

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LongSAGE profiling of nine human embryonic stem cell lines.

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References

Alizadeh A, Eisen M, Davis R, Ma C, Lossos I, Rosenwald A . Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000; 403(6769):503-11. DOI: 10.1038/35000501. View

Ross D, Scherf U, Eisen M, Perou C, Rees C, Spellman P . Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000; 24(3):227-35. DOI: 10.1038/73432. View

Schuchhardt J, Beule D, Malik A, Wolski E, EICKHOFF H, Lehrach H . Normalization strategies for cDNA microarrays. Nucleic Acids Res. 2000; 28(10):E47. PMC: 105386. DOI: 10.1093/nar/28.10.e47. View

Perou C, Sorlie T, Eisen M, van de Rijn M, Jeffrey S, Rees C . Molecular portraits of human breast tumours. Nature. 2000; 406(6797):747-52. DOI: 10.1038/35021093. View

Lee M, Kuo F, Whitmore G, Sklar J . Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A. 2000; 97(18):9834-9. PMC: 27599. DOI: 10.1073/pnas.97.18.9834. View

Marton M, DeRisi J, Bennett H, Iyer V, Meyer M, Roberts C . Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998; 4(11):1293-301. DOI: 10.1038/3282. View

Luo J, Duggan D, Chen Y, Sauvageot J, Ewing C, Bittner M . Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Cancer Res. 2001; 61(12):4683-8. View

Tseng G, Oh M, Rohlin L, Liao J, Wong W . Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 2001; 29(12):2549-57. PMC: 55725. DOI: 10.1093/nar/29.12.2549. View

Wang X, Ghosh S, Guo S . Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Res. 2001; 29(15):E75-5. PMC: 55840. DOI: 10.1093/nar/29.15.e75. View

10.

Sorlie T, Perou C, Tibshirani R, Aas T, Geisler S, Johnsen H . Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001; 98(19):10869-74. PMC: 58566. DOI: 10.1073/pnas.191367098. View

11.

Yang M, Ruan Q, Yang J, Eckenrode S, Wu S, McIndoe R . A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiol Genomics. 2001; 7(1):45-53. DOI: 10.1152/physiolgenomics.00020.2001. View

12.

Yue H, Eastman P, Wang B, Minor J, Doctolero M, Nuttall R . An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 2001; 29(8):E41-1. PMC: 31325. DOI: 10.1093/nar/29.8.e41. View