Research > Microarray Data Analysis > CDNA
Image Analysis Spot: is an image analysis program for microarray images

References: Y. H. Yang, M. J. Buckley, S. Dudoit, and T. P. Speed (2002)
Comparison of methods for image analysis on cDNA microarray data.
Journal of Computational and Graphical Statistics, Vol. 11, No. 1, p. 108--136. link Spot manual
Normalization SMA: a package in the R language for cDNA microarray analysis

marrayNorm: a package within Bioconductor

Reference: S. Dudoit, Y. H. Yang, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed (2002)
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.
Nucleic Acids Research, Vol. 30, No. 4, e15. link
Other good references
  • Differential Expression:
    S. Dudoit, Y. H. Yang, T. P. Speed, and M. J. Callow (2002)
    Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.
    Statistica Sinica, Vol. 12, No. 1, p. 111--139. pdf
  • Classification
    S. Dudoit, J. Fridlyand, and T. P. Speed (2002)
    Comparison of discrimination methods for the classification of tumors using gene expression data
    Journal of the American Statistical Association, Vol. 97, No. 457, p. 77--87. Preprint #576

  • Other References
    Statistical Analysis of Gene Expression Microarray Data (2003) by T. P. Speed (Editor)
    CRC press Amazon BN
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This page prepared by Yu Chuan Tai