Improvement of Optical Correction for GCRMA in Affymetrix Array

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研究生：	謝明潔 Ming-Jie Hsieh
論文名稱：	Improvement of Optical Correction for GCRMA in Affymetrix Array 改善GCRMA中移除生物晶片光學干擾的方法
指導教授：	謝文萍 Wen-Ping Hsieh
口試委員:
學位類別：	碩士 Master
系所名稱：	理學院 - 統計學研究所 Institute of Statistics
論文出版年：	2006
畢業學年度：	94
語文別：	英文
論文頁數：	36
中文關鍵詞：	GCRMA 、Optical 、Affymetrix
相關次數：	點閱：1 下載：0
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High density oligonucleotide microarrays have been one of the most useful techniques which widely used in genomic science. GCRMA is designed to measure the gene expression on the microarrays, which uses a very simple global estimator for the optical noise, and we suggest correcting the optical noise in another location-specific manner in this study. We found the base-effects estimated by location specific optical adjusted data are stronger than those by global optical adjusted data, and there is a little improvement in accuracy for several spike-in probe sets on the used Affymetrix array.

TABLE OF CONTENTS
1. Introduction...................................1
2. Methods.........................................4
    2.1 RMA........................................4
    2.2 GCRMA......................................4
    2.3 The Location Specific Optical Correction in MAS5.0 ............................................6
    2.4 Combination of Location Specific Correction and GCRMA..............................................7
3. Data............................................8
4. Results.........................................9
    4.1 Probe Affinity.............................9
        4.1.1 Estimation of Probe Affinity.........9
        4.1.2 The Reference Probe Affinities.......10
        4.1.3 The Local Probe Affinities...........10
    4.2 Summarize the Gene Expression Measures.....11
        4.2.1 GCRMA with Global Optical Noise and the Reference Probe affinities.........................11
        4.2.2 GCRMA with Global Optical Noise and the Local Probe Affinities...................................12
        4.2.3 Gene Expression Summary with Location Specific Optical Noise and Reference Probe Affinities.....12
        4.2.4 Gene Expression Summary with Location Specific Optical Noise and Local Probe Affinities......12
    4.3 Comparisons of Optical correction..............12
    4.4 Comparisons in Gene Expression Measures........13
        4.4.1 The Accuracy in Gene Expression..........13
        4.4.2 The Precision of Gene Expression Summary....18
        4.4.3. Comparison in Fold Change..................25
    4.5 Data Transformation...............................29
5. Conclusion.............................................35
6. Reference..............................................36

                                

Reference
Affymetrix Inc. New statistical algorithms for monitoring gene expression on Gene Chip@ probe arrays. 2001.
Affymetrix Inc. Statistical algorithms description document. 2002.
Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18 Suppl 1:S96-104.
Irizarry, RA. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.
Naef F, Magnasco MO. Solving the riddle of the bright mismatches labeling and effective binding in oligonucleotide arrays. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906.
Wu Z, Irizarry R. A. A model based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association. 2004; Vol. 99, Number 468, pp. 909-917(9).

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