Application of a correlation correction factor in a microarray cross-platform reproducibility study

被引：3

作者：

Archer, Kellie J. ^{[1
,4
]}

Dumur, Catherine I. ^{[2
]}

Taylor, G. Scott ^{[3
]}

Chaplin, Michael D. ^{[4
]}

Guiseppi-Elie, Anthony ^{[3
]}

Grant, Geraldine ^{[5
]}

Ferreira-Gonzalez, Andrea

Garrett, Carleton T. ^{[2
]}

机构：

[1] Virginia Commonwealth Univ, Dept Biostat, Richmond, VA 23284 USA

[2] Virginia Commonwealth Univ, Dept Pathol, Richmond, VA USA

[3] Virginia Commonwealth Univ, Sch Engn, Ctr Bioelect Biosensors & Biochips, Richmond, VA USA

[4] Virginia Commonwealth Univ, Ctr Study Biol Complex, Richmond, VA USA

[5] George Mason Univ, Dept Mol Biol & Microbiol, Manassas, VA USA

来源：

BMC BIOINFORMATICS | 2007年 / 8卷

关键词：

GENE-EXPRESSION MEASUREMENTS; OLIGONUCLEOTIDE ARRAYS; CDNA; AFFYMETRIX; NORMALIZATION; METAANALYSIS; CONCORDANCE; PERFORMANCE; PROFILES; GENERATIONS;

D O I：

10.1186/1471-2105-8-447

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. Results: In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra- platform reproducibility. We also examine cross-platform reproducibility using Pearson's correlation. Additionally, we previously developed a correction factor for Pearson's correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement error by estimating the "disattenuated" correlation substantially improves cross-platform correlations. Conclusion: When estimating cross-platform correlation, it is essential to thoroughly evaluate intra- platform reproducibility as a first step. In addition, since measurement error is present in microarray gene expression data, methods to correct for attenuation are useful in decreasing the bias in cross-platform correlation estimates.

引用

页数：13

共 61 条

[1]

Allison David B., 2006, V15, P1

[2]

ARCHER KJ, 2007, IN PRESS STAT MED, DOI DOI 10.1002/S272984

[3] Spotted long oligonucleotide arrays for human gene expression analysis [J].

Barczak, A ;

Rodriguez, MW ;

Hanspers, K ;

Koth, LL ;

Tai, YC ;

Bolstad, BM ;

Speed, TP ;

Erle, DJ .

GENOME RESEARCH, 2003, 13 (07) :1775-1785

[4]

BARRETT T, 1956, NUCLEIC ACIDS RES, V33, pD562

[5] MatchMiner: a tool for batch navigation among gene and gene product identifiers [J].

Bussey, KJ ;

Kane, D ;

Sunshine, M ;

Narasimhan, S ;

Nishizuka, S ;

Reinhold, WC ;

Zeeberg, B ;

Ajay ;

Weinstein, JN .

GENOME BIOLOGY, 2003, 4 (04)

[6] Evaluation of DNA microarray results with quantitative gene expression platforms [J].

Canales, Roger D. ;

Luo, Yuling ;

Willey, James C. ;

Austermiller, Bradley ;

Barbacioru, Catalin C. ;

Boysen, Cecilie ;

Hunkapiller, Kathryn ;

Jensen, Roderick V. ;

Knight, Charles R. ;

Lee, Kathleen Y. ;

Ma, Yunqing ;

Maqsodi, Botoul ;

Papallo, Adam ;

Peters, Elizabeth Herness ;

Poulter, Karen ;

Ruppel, Patricia L. ;

Samaha, Raymond R. ;

Shi, Leming ;

Yang, Wen ;

Zhang, Lu ;

Goodsaid, Federico M. .

NATURE BIOTECHNOLOGY, 2006, 24 (09) :1115-1122

[7]

Carroll R.J., 2006, MEASURMENT ERROR NON

[8] Redefinition of affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements [J].

Carter, SL ;

Eklund, AC ;

Mecham, BH ;

Kohane, IS ;

Szallasi, Z .

BMC BIOINFORMATICS, 2005, 6 (1)

[9]

Cope L., 2004, STAT APPL GENET MOL, V3, P29, DOI [DOI 10.2202/1544-6115.1046, 10.2202/1544-6115.1046]

[10]

Dudoit S, 2002, STAT SINICA, V12, P111

← 1 2 3 4 5 6 7 →