The Weibull distribution based normalization method for affymetrix gene expression microarray data

Reija Autio; Sami Kilpinen; Matti Saarela; Sampsa Hautaniemi; Olli Kallioniemi; Jaakko Astola

doi:10.1109/GENSIPS.2006.353130

The Weibull distribution based normalization method for affymetrix gene expression microarray data

Reija Autio, Sami Kilpinen, Matti Saarela, Sampsa Hautaniemi, Olli Kallioniemi, Jaakko Astola

VTT Technical Research Centre of Finland

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

1 Citation (Scopus)

Abstract

Affymetrix human gene expression microarrays are widely used in gene expression analysis. However, the comparability of data analyzed in different laboratories is not self-evident hindering integration of multiple data sets. In this study, we introduce a novel normalization method, Weibull distribution based normalization that makes the data from different laboratories easier to integrate and compare. The method normalizes the samples by correcting the ML-estimates of the parameters of Weibull distribution to be the same in every sample of the same array generation. The effects of the Weibull distribution based normalization were studied by comparing the distributions of the samples, examining the deviations of expression levels of housekeeping genes, and clustering the data.

Original language	English
Title of host publication	2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006
Publisher	IEEE Institute of Electrical and Electronic Engineers
Pages	9-10
ISBN (Electronic)	1-4244-0385-5
ISBN (Print)	1-4244-0384-7
DOIs	https://doi.org/10.1109/GENSIPS.2006.353130
Publication status	Published - 2006
MoE publication type	A4 Article in a conference publication
Event	2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006 - College Station, United States Duration: 28 May 2006 → 30 May 2006

Conference

Conference	2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006
Country/Territory	United States
City	College Station
Period	28/05/06 → 30/05/06

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10.1109/GENSIPS.2006.353130

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Autio, R., Kilpinen, S., Saarela, M., Hautaniemi, S., Kallioniemi, O., & Astola, J. (2006). The Weibull distribution based normalization method for affymetrix gene expression microarray data. In 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006 (pp. 9-10). IEEE Institute of Electrical and Electronic Engineers. https://doi.org/10.1109/GENSIPS.2006.353130

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title = "The Weibull distribution based normalization method for affymetrix gene expression microarray data",

abstract = "Affymetrix human gene expression microarrays are widely used in gene expression analysis. However, the comparability of data analyzed in different laboratories is not self-evident hindering integration of multiple data sets. In this study, we introduce a novel normalization method, Weibull distribution based normalization that makes the data from different laboratories easier to integrate and compare. The method normalizes the samples by correcting the ML-estimates of the parameters of Weibull distribution to be the same in every sample of the same array generation. The effects of the Weibull distribution based normalization were studied by comparing the distributions of the samples, examining the deviations of expression levels of housekeeping genes, and clustering the data.",

author = "Reija Autio and Sami Kilpinen and Matti Saarela and Sampsa Hautaniemi and Olli Kallioniemi and Jaakko Astola",

year = "2006",

doi = "10.1109/GENSIPS.2006.353130",

language = "English",

isbn = "1-4244-0384-7",

pages = "9--10",

booktitle = "2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006",

publisher = "IEEE Institute of Electrical and Electronic Engineers",

address = "United States",

note = "2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006 ; Conference date: 28-05-2006 Through 30-05-2006",

}

Autio, R, Kilpinen, S, Saarela, M, Hautaniemi, S, Kallioniemi, O & Astola, J 2006, The Weibull distribution based normalization method for affymetrix gene expression microarray data. in 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006. IEEE Institute of Electrical and Electronic Engineers, pp. 9-10, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006, College Station, Texas, United States, 28/05/06. https://doi.org/10.1109/GENSIPS.2006.353130

The Weibull distribution based normalization method for affymetrix gene expression microarray data. / Autio, Reija; Kilpinen, Sami; Saarela, Matti et al.

2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006. IEEE Institute of Electrical and Electronic Engineers, 2006. p. 9-10.

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

TY - GEN

T1 - The Weibull distribution based normalization method for affymetrix gene expression microarray data

AU - Autio, Reija

AU - Kilpinen, Sami

AU - Saarela, Matti

AU - Hautaniemi, Sampsa

AU - Kallioniemi, Olli

AU - Astola, Jaakko

PY - 2006

Y1 - 2006

N2 - Affymetrix human gene expression microarrays are widely used in gene expression analysis. However, the comparability of data analyzed in different laboratories is not self-evident hindering integration of multiple data sets. In this study, we introduce a novel normalization method, Weibull distribution based normalization that makes the data from different laboratories easier to integrate and compare. The method normalizes the samples by correcting the ML-estimates of the parameters of Weibull distribution to be the same in every sample of the same array generation. The effects of the Weibull distribution based normalization were studied by comparing the distributions of the samples, examining the deviations of expression levels of housekeeping genes, and clustering the data.

AB - Affymetrix human gene expression microarrays are widely used in gene expression analysis. However, the comparability of data analyzed in different laboratories is not self-evident hindering integration of multiple data sets. In this study, we introduce a novel normalization method, Weibull distribution based normalization that makes the data from different laboratories easier to integrate and compare. The method normalizes the samples by correcting the ML-estimates of the parameters of Weibull distribution to be the same in every sample of the same array generation. The effects of the Weibull distribution based normalization were studied by comparing the distributions of the samples, examining the deviations of expression levels of housekeeping genes, and clustering the data.

U2 - 10.1109/GENSIPS.2006.353130

DO - 10.1109/GENSIPS.2006.353130

M3 - Conference article in proceedings

SN - 1-4244-0384-7

SP - 9

EP - 10

BT - 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006

PB - IEEE Institute of Electrical and Electronic Engineers

T2 - 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006

Y2 - 28 May 2006 through 30 May 2006

ER -

The Weibull distribution based normalization method for affymetrix gene expression microarray data

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