Bernoulli

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  • Volume 10, Number 6 (2004), 943-949.

Intensity-dependent normalization in microarray analysis: a note of concern

Mei-Ling Ting Lee and George A. Whitmore

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Abstract

We discuss the concern that intensity-dependent normalization can give biased estimates of differential expression and, therefore, can misclassify some moderately important genes as unexpressed.

Article information

Source
Bernoulli Volume 10, Number 6 (2004), 943-949.

Dates
First available in Project Euclid: 21 January 2005

Permanent link to this document
http://projecteuclid.org/euclid.bj/1106314844

Digital Object Identifier
doi:10.3150/bj/1106314844

Mathematical Reviews number (MathSciNet)
MR2108037

Zentralblatt MATH identifier
1064.62111

Keywords
gene expression intensity dependence MA-plot microarray normalization

Citation

Ting Lee, Mei-Ling; Whitmore, George A. Intensity-dependent normalization in microarray analysis: a note of concern. Bernoulli 10 (2004), no. 6, 943--949. doi:10.3150/bj/1106314844. http://projecteuclid.org/euclid.bj/1106314844.


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References

  • [1] Dudoit, S., Yang Y.H., Callow, M.J. and Speed, T.P. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statist. Sinica, 12, 111-139.
    Mathematical Reviews (MathSciNet): MR1894191
    Zentralblatt MATH: 1004.62088
  • [2] Eisen, M.B. and Brown, P.O. (1999) DNA arrays for analysis of gene expression. In S.M. Weissman (ed.), cDNA Preparation and Characterization, Methods in Enzymology 303, pp. 179-205. San Diego, CA: Academic Press.
  • [3] Kerr, M.K. and Churchill, G.A. (2001) Experimental design issues for gene expression microarrays. Biostatistics, 2, 183-201.
    Digital Object Identifier: doi:10.1093/biostatistics/2.2.183
  • [4] Kerr, M.K., Martin, M. and Churchill, G.A. (2001) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
    Digital Object Identifier: doi:10.1089/10665270050514954
  • [5] Lee, M.-L.T., Lu, W., Whitmore, G.A. and Beier, D. (2002) Models for microarray gene expression data. J. Biopharmaceutical Statist., 12(1), 1-19. Abstract can also be found in the ISI/STMA publication
    URL: Link to item
    Digital Object Identifier: doi:10.1081/BIP-120005737
  • [6] Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J. and Speed, T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30(4), e15.

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