BIOS 567: Statistical Methods for Microarray Data
Overview of Microarray Technology
- DNA microarrays have given geneticists and molecular biologists access to more
data than ever before. But do these researchers have the statistical know-how
to cope? Claire Tilstone. Nature 424, 610 - 612 (07 August 2003) (link)
- Bioinformatics
needs to adopt statistical thinking. Editorial, (2001) Bioinformatics:
17, 389-390. (link)
- Biology Introduction Source: European Bioinformatics Institute. (link)
Software
- Bioconductor (link)
- The comprehensive R archive network (link)
Image Analysis
- Comparison
of Methods for Image Analysis on cDNA Microarray Data. Yang, Y.H., Buckley,
M.J., Dudoit, S., Speed, T.P. (2002) Journal of Computational and Graphical
Statistics 11(1):108-136. (link)
Normalization
- Normalization
for cDNA microarray data: a robust composite method addressing single and
multiple slide systematic variation. Yee Hwa Yang, Sandrine Dudoit, Percy
Luu, David M. Lin, Vivian Peng, John Ngai, and Terence P. Speed. Nucleic
Acids Res. 2002 Feb 15;30(4):e15. (link)
- A
comparison of normalization methods for high density oligonucleotide array
data based on variance and bias. B.M. Bolstad, R.A Irizarry, M. Åstrand,
and T.P. Speed. Bioinformatics 2003 19: 185-193. (link)
Expression Summaries
- Exploration,
normalization, and summaries of high density oligonucleotide array probe
level data. Rafael A. Irizarry, Bridget Hobbs, Francois Collin, Yasmin
D. Beazer-Barclay, Kristen J. Antonellis, Uwe Scherf, and Terence P. Speed.
Biostatistics 2003 4: 249-264. (link)
- Robust
estimators for expression analysis Earl Hubbell, Wei-Min Liu, and Rui
Mei Bioinformatics 2002 18: 1585-1592. (link)
- 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,
C. A. Harrington, M.-h. Ho, J. Baid, and S. P. Smeekens. Bioinformatics
2002 18: 1593-1599. (link)
Quality assessment of microarrays
- affy - analysis of Affymetrix GeneChip data at the probe level. L. Gautier, L. Cope, B.M. Bolstad, R.A. Irizarry. Bioinformatics
2004 20:307-315. (link)
- Array-A-Lizer: A serial DNA microarray quality analyzer. A. Petri, J. Fleckner, M.W. Matthiessen. BMC Bioinformatics
2004 5:12. (link)
Unsupervised learning methods
- Cluster analysis and display of genone-wide expression patterns. MB Eisen, PT Spellman, PO Brown, D Botstein. PNAS 1998 95:14863-14868. (link)
Supervised learning methods
- Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. S Dudoit, YH Yang, MJ Callow, TP Speed. Statistica Sinica 2002 12:111-139. (link)
- Expression profiling - best practices for data generation and interpretation in clinical trials. The Tumor Analysis Best Practices Working Group. Nature Reviews 2004 5:229-238. (link)
Experimental Design
- Design
of Studies Using DNA Microarrays, Richard Simon, Michael D. Radmacher,
Kevin Dobbin. (link)
- Importance of
replication in microarray gene expression studies:Statistical methods and
evidence from repetitive cDNA hybridizations, Mei-Ling Ting Lee, Frank
C. Kuo, G. A. Whitmore, and Jeffrey Sklar. (2000) PNAS 97(18):9834-9839. (link)
