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Significance Analysis of Dose-Response Microarray Data

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Modeling Dose-Response Microarray Data in Early Drug Development Experiments Using R

Part of the book series: Use R! ((USE R))

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Abstract

The significance analysis of microarrays (SAM) Tusher et al. (Proc Natl Acad Sci 98:5116–5121, 2001) is a widely used testing procedure that estimates the FDR by using permutations under the assumption that all null hypotheses are true. The procedure consists of three components: (1) the adjusted test statistics, (2) an approximation of the distribution of the test statistics based on permutations, and (3) the control of the FDR. In Chap. 8, we discuss the implementation SAM for the setting of dose-response microarray experiments and illustrate how to use the IsoGene package for SAM.

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References

  • Chu, G., Li, J., Narasimhan, B., Tibshirani, R., & Tusher, V. (2011). SAM: “Significance Analysis of Microarrays” users guide and technical document. http://www-stat.stanford.edu/~tibs/SAM/sam.pdf.

  • Tusher, V. G., Tibshirani, R., & Chu, G. (2001). Significance analysis of microarrys applied to the ionizing radiation response. Proceedings of the National Academy of Sciences, 98, 5116–5121.

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Authors and Affiliations

  1. Veterinary Medicine Research and Development, Pfizer Animal Health, Zaventem, Belgium

    Dan Lin

  2. Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Center for Statistics (CenStat), Hasselt University, Diepenbeek, Belgium

    Ziv Shkedy

  3. Janssen Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium

    Hinrich W. H. Göhlmann, An De Bondt, Luc Bijnens & Willem Talloen

  4. Biostatistics and Programming, Jansenn Pharmaceutical Companies of Johnson & Johnson, Raritan, NJ, USA

    Dhammika Amaratunga

Authors
  1. Dan Lin
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  2. Ziv Shkedy
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  3. Hinrich W. H. Göhlmann
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  4. An De Bondt
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  5. Luc Bijnens
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  6. Dhammika Amaratunga
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  7. Willem Talloen
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Corresponding author

Correspondence to Dan Lin .

Editor information

Editors and Affiliations

  1. , VMRD, Pfizer Animal Health, Hoge Wei 1, Zaventem, 1930, Belgium

    Dan Lin

  2. Center for Statistics, Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium

    Ziv Shkedy

  3. , Department of Statistics and, School of Mathematical Sciences, Ramat Aviv, Tel Aviv, 69978, Israel

    Daniel Yekutieli

  4. Johnson & Johnson, Route 202 1000, Raritan, 08869, New Jersey, USA

    Dhammika Amaratunga

  5. , Biostatistics and Programming Center of, Janssen Pharmaceutica, Turnhoutseweg 30, Beerse, 2340, Belgium

    Luc Bijnens

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© 2012 Springer-Verlag Berlin Heidelberg

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Lin, D. et al. (2012). Significance Analysis of Dose-Response Microarray Data. In: Lin, D., Shkedy, Z., Yekutieli, D., Amaratunga, D., Bijnens, L. (eds) Modeling Dose-Response Microarray Data in Early Drug Development Experiments Using R. Use R!. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24007-2_8

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