Analysis of high density expression microarrays with signed-rank call algorithms

W. M. Liu, R. Mei, X. Di, T. B. Ryder, E. Hubbell, S. Dee, T. A. Webster, Christina (Chris) Harrington, M. H. Ho, J. Baid, S. P. Smeekens

    Research output: Contribution to journalArticle

    340 Citations (Scopus)

    Abstract

    Motivation: We consider the detection of expressed genes and the comparison of them in different experiments with the high-density oligonucleotide microarrays. The results are summarized as the detection calls and comparison calls, and they should be robust against data outliers over a wide target concentration range. It is also helpful to provide parameters that can be adjusted by the user to balance specificity and sensitivity under various experimental conditions. Results: We present rank-based algorithms for making detection and comparison calls on expression microarrays. The detection call algorithm utilizes the discrimination scores. The comparison call algorithm utilizes intensity differences. Both algorithms are based on Wilcoxon's signed-rank test. Several parameters in the algorithms can be adjusted by the user to alter levels of specificity and sensitivity. The algorithms were developed and analyzed using spiked-in genes arrayed in a Latin square format. In the call process, p-values are calculated to give a confidence level for the pertinent hypotheses. For comparison calls made between two arrays, two primary normalization factors are defined. To overcome the difficulty that constant normalization factors do not fit all probe sets, we perturb these primary normalization factors and make increasing or decreasing calls only if all resulting p-values fall within a defined critical region. Our algorithms also automatically handle scanner saturation.

    Original languageEnglish (US)
    Pages (from-to)1593-1599
    Number of pages7
    JournalBioinformatics
    Volume18
    Issue number12
    DOIs
    StatePublished - Dec 1 2002

    Fingerprint

    Microarrays
    Signed
    Microarray
    Normalization
    p-Value
    Specificity
    Genes
    Wilcoxon Signed Rank Test
    Gene
    Sensitivity and Specificity
    Critical region
    Magic square
    Oligonucleotides
    Confidence Level
    Nonparametric Statistics
    Scanner
    Oligonucleotide Array Sequence Analysis
    Outlier
    Discrimination
    Saturation

    ASJC Scopus subject areas

    • Clinical Biochemistry
    • Computer Science Applications
    • Computational Theory and Mathematics

    Cite this

    Liu, W. M., Mei, R., Di, X., Ryder, T. B., Hubbell, E., Dee, S., ... Smeekens, S. P. (2002). Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics, 18(12), 1593-1599. https://doi.org/10.1093/bioinformatics/18.12.1593

    Analysis of high density expression microarrays with signed-rank call algorithms. / Liu, W. M.; Mei, R.; Di, X.; Ryder, T. B.; Hubbell, E.; Dee, S.; Webster, T. A.; Harrington, Christina (Chris); Ho, M. H.; Baid, J.; Smeekens, S. P.

    In: Bioinformatics, Vol. 18, No. 12, 01.12.2002, p. 1593-1599.

    Research output: Contribution to journalArticle

    Liu, WM, Mei, R, Di, X, Ryder, TB, Hubbell, E, Dee, S, Webster, TA, Harrington, CC, Ho, MH, Baid, J & Smeekens, SP 2002, 'Analysis of high density expression microarrays with signed-rank call algorithms', Bioinformatics, vol. 18, no. 12, pp. 1593-1599. https://doi.org/10.1093/bioinformatics/18.12.1593
    Liu, W. M. ; Mei, R. ; Di, X. ; Ryder, T. B. ; Hubbell, E. ; Dee, S. ; Webster, T. A. ; Harrington, Christina (Chris) ; Ho, M. H. ; Baid, J. ; Smeekens, S. P. / Analysis of high density expression microarrays with signed-rank call algorithms. In: Bioinformatics. 2002 ; Vol. 18, No. 12. pp. 1593-1599.
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