Genelogic Workshop on Low Level Analysis of Affymetrix Genechip® data

Held on Nov 19, 2001 at Bethesda, MD

Terry Speed's SUMMARY of meeting.

Session 1: Image analysis/Background adjustment/Expression

Harry Zuzan (GLGC): Estimating probe cell locations. Pdf slides

Felix Naef (Rockefeller): Excursions into GeneChip data analysis Powerpoint slides

Earl Hubbell (Affymetrix): Estimating Signal with Next Generation Affymetrix Software. Powerpoint slides

Session 2: Model-based expression indices.

Cheng Li (Harvard) Model-based Saturation Handling Powerpoint slides

Dan Holder (Merck): Quantitation of gene expression: a SAFER approach. Powerpoint slides

Fred Wright (Ohio State) Theoretical and experimental comparisons of gene expression indexes for oligonucleotide microarrays. Powerpoint slides

Session 3: Normalization/Comparisons of expression indices

Andrew Hill (Genetics Institute) Evaluation of Affymetrix array normalization procedures based on spiked cRNAs. Powerpoint slides

Magnus Astrand (Astra Zeneca) Normalization of PM values. PDF file

Peter Munson (NIH) A "Consistency" Test for Determining the Significance of Gene Expression Changes on Replicate Samples and Two Convenient Variance-stabilizing Transformations Powerpoint slides

Rafael Irizarry (Johns Hopkins) Bias, variance and fit for three measures of expression: AvDiff, Li & Wong's, AvLog(PM-bg). Powerpoint slides

Session 4: Quality assessment

Peter Haberl (GeneData) A Routine Approach to Quality Control Powerpoint slides

Michael Elashoff (GLGC) Automated Chip QC. Powerpoint slides

Bill Craven (GLGC) The Gene Logic Dilution Series. Powerpoint slides

Additional materials

Astrand, Magnus (2001) Normalizing Oligonucleotide Arrays Unpublished Manuscript

Bolstad, B (2001) Probe Level Quantile Normalization for High Density Oligonucleotide Array Data Unpublished Manuscript Pdf file

Holder, Daniel, Richard F. Raubertas, V. Bill Pikounis, Vladimir Svetnkik and Keith Soper (2001) Statistical Analysis of High Density Oligonucleotide arrays: A SAFER approach Unpublished Manuscript

Irizarry, RA, Hobbs, B, and Speed, T (2001) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Manuscript in preparation. Full text Figures

Bibliography of papers by participants

Felix Naef, Daniel A. Lim, Nila Patil, Marcelo O. Magnasco (2001) From features to expression: High-density oligonucleotide array analysis revisited LANL e-print physics/0102010

Cheng Li and Wing Hung Wong (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application, Genome Biology 2(8): research0032.1-0032.11 Full text

Cheng Li and Wing Hung Wong (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl. Acad. Sci. Vol. 98, 31-36. Full text

Lemon, WJ, Palatini, JT, Krahe, R, Wright, FA, (2001) Comparison of gene expression estimators for oligonucleotide arrays, submitted 2001. Fulltext Supplementary Material

Andrew A Hill, Eugene L Brown, Maryann Z Whitley, Greg Tucker-Kellogg, Craig P Hunter, Donna K Slonim (2001) Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls Genome Biology 2(12): research0055.1-0055.13 Online access

Schadt EE, Li C, Su C, Wong WH. (2000) Analyzing high-density oligonucleotide gene expression array data, J. Cellular Biochemistry, 80, 192-202 Full text

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Last modified: Wed Dec 5 16:17:25 PST 2001
zarray@stat.berkeley.edu

contact Terry Speed's
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