Development, Implementation and Testing of a DNA Microarray Test Suite

1
Development, Implementation and Testing of a DNA
Microarray Test Suite

• Ehsanul Haque
• Mentors
• Dr. Cecilie Boysen
• Dr. Jim Breaux
• ViaLogy Corp.

2
Outline

• Purpose
• Background
• Datasets
• Algorithms
• Results
• Conclusion

3
Purpose

• 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

4
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
5
From image to gene level data
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
6
Datasets
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
7
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)
Other
Output
8
Algorithm
User File
Function RA (Rela. Accu.)
File list parameters
Function TABLE.IN
Using a loop, calls function TABLE.IN to work on
the User File list of input datasets
Calls other functions, parses different formats
of data-sets and provides function RA with the
required table.
Calculates Mean SD
Plots Conc. vs. Mean Intensity
Replaces zero values
Plots Slope vs. Average of mean intensity
Creates a list of Median Slope
Calculates Slope and Ave. of mean intensities
Method A Method B Method C Method D Slope
0.497897086864 0.394078146688 0.33660070237
0.211275056257
9
CV Plot Three Replicates A, B C
10
CV Plot With fitted line
11
8 Dilutions Mean Intensity vs. Concentration
12
Slope vs. Mean Intensity
13
Median Slope
14
Results
15
Conclusion

• 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.

16
Reference Acknowledgment

• 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)