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Development, Implementation and Testing of a DNA Microarray Test Suite. Ehsanul Haque Mentors: Dr. Cecilie Boysen Dr. Jim Breaux ViaLogy Corp. Outline. Purpose Background Datasets Algorithms Results Conclusion. Purpose. To design tests to assess the results from

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Development implementation and testing of a dna microarray test suite

Development, Implementation and Testing of a DNA Microarray Test Suite

Ehsanul Haque

Mentors:

Dr. Cecilie Boysen

Dr. Jim Breaux

ViaLogy Corp.


Outline
Outline Test Suite

  • Purpose

  • Background

  • Datasets

  • Algorithms

  • Results

  • Conclusion


Purpose
Purpose Test Suite

To design tests to assess the results from

  • Different microarray data analysis services

    • VMAxS, GCOS

  • Different updates of the same data analysis service

    • VMAxS_V1, VMAxS_V2, VMAxS_V3, VMAxS_V4

  • Different background correction, normalization and summarization methods

    • VMAxS, PLIER, RMA, dCHIP

  • Different technologies of microarray data analysis

    • Affymetrix, ABI, Agilent, GE Healthcare, Illumina


  • Background

    VMAxS Test Suite

    Signal Detection via

    QRI

    Background

    Quantum Resonance Interferometry (QRI)– Active Signal Processing

    VMAxS RA Report

    (Resonance Amplitude)

    • Probe level signal data

    • 11-20 probe per gene

    • 1 expression value per gene

      (if from Affymetrix system)

    DAT or raw image file

    Only raw data files accepted


    From image to gene level data
    From image to gene level data Test Suite

    Raw pixel level data

    Image analysis

    VMAxS/GCOS

    Probe level data

    Background correction

    Normalization

    Summarization (PM/MM)

    VMAxS/MAS5.0/PLIER/RMA

    Gene level data


    Datasets
    Datasets Test Suite

    Each Dataset stems from the same raw AffymetrixGeneChip .dat files

    Method A

    3 Replicates * 8 Dilutions

    24 Samples

    Method B

    3 Replicates * 8 Dilutions

    24 Samples

    .DAT File

    Method C

    3 Replicates * 8 Dilutions

    24 Samples

    Method D

    3 Replicates * 8 Dilutions

    24 Samples

    GeneChip family Human 2A: 54676 genes


    Test suite r scripting
    Test Suite Test Suite[R scripting]

    User File

    Function CV

    (Coefficient of Variance)

    File list & parameters

    Master Function

    Function RA

    (Relative Accuracy)

    Function DEG

    (Differential Expressed Gene)

    Output

    Other


    Algorithm
    Algorithm Test Suite

    User File

    Function RA

    (Rela. Accu.)

    File list & parameters

    Using a loop, calls function TABLE.IN to work on the User File list of input datasets

    Function

    TABLE.IN

    Calls other functions, parses different formats of data-sets and provides function RA with the required table.

    Replaces zero values

    Calculates

    Mean & SD

    Plots

    Conc. vs. Mean Intensity

    Creates a list of

    Median Slope

    Plots Slope vs.

    Average of mean intensity

    Calculates Slope and

    Ave. of mean intensities

    Method A Method B Method C Method D

    Slope 0.497897086864 0.394078146688 0.33660070237 0.211275056257


    Cv plot three replicates a b c
    CV Plot Test SuiteThree Replicates A, B & C


    Cv plot with fitted line
    CV Plot Test SuiteWith fitted line


    8 dilutions mean intensity vs concentration
    8 Dilutions Test SuiteMean Intensity vs. Concentration



    Median slope
    Median Slope Test Suite


    Results
    Results Test Suite


    Conclusion
    Conclusion Test Suite

    • Developed and implemented two tests in R

      • CV & RA (relative accuracy)

    • Tested 2 X 4 datasets

      • Different parameters of the same analysis method

      • Different normalization methods

    • More tests are needed to draw a better conclusion about the data.


    Reference acknowledgment
    Reference & Acknowledgment Test Suite

    References:

    • Zhijin Wu el al, A Model Based Background Adjustment of Oligonucleotide Expression Arrays, Johns Hopkins University, Dept of Biostatistics Working Papers, 2004, paper 1

    • Irizarry et al, Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics (2003), 4, 2, pp. 249-264

    • Cope et al, A Benchmark of Affymetrix GeneChip Expression Measures, Bioinformatics, Vol. 1 no. 1 2003, pp. 1-10

      Acknowledgements:

    • Dr. Cecilie Boysen

    • Dr. Jim Breaux

      - Vialogy

    • Southern California Bioinformatics Summer Institute (SoCalBSI)

    • National Institute of Health (NIH)


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