BioMicroCenter:Education

The BioMicro Center offers formal training programs for commercial software as well as office hours during which Center staff help with data analysis. The Center also offers a BioMicroCenter:microarray club every two weeks with expert speakers from various institutes and industries. In addition to the microarray club, the Center sponsors an annual conference with a focus on computational and systems biology.

The BioMicro Center offers a link to current BioMicroCenter:microarray publications though the BioMicroCenter:pubmed search engine.

The BioMicro Center provides information to users regarding current normalization strategies used in the field. References that our users have found useful are listed below.

Two color array normalization
BioMicroCenter:Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments

(Sandrine Dudoit, Yee Hwa Yang, Matthew J. Callow, and Terence P. Speed) 

Affymetrix (DChip)
BioMicroCenter:Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection

(Cheng Li and Wing Hung Wong) PNAS, 2001 

BioMicroCenter:Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application

(Cheng Li and Wing Hung Wong) Genome Biology, 2001 

Basic Research Applications of DChip
BioMicroCenter:“Stemness”: Transcriptional Pro.ling of Embryonic and Adult Stem Cells (Miguel Ramalho-Santos, Soonsang Yoon, Yumi Matsuzaki, Richard C. Mulligan, Douglas A. Melton) Science, 2002 

Affymetrix (RMA)
BioMicroCenter: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, Terence P. Speed) 

BioMicroCenter:Summaries of Affymetrix GeneChip probe level data

(Rafael A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed) Nucleic Acids Research, 2003 

BioMicroCenter:A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

(B. M. Bolstad, R. A. Irizarry, M. Astrand and T. P. Speed) Bioinformatics, 2003 

Gene Ontology
BioMicroCenter:GOstat: Find statistically overrepresented Gene Ontologies within a group of genes

(Beissbarth T, Speed TP) Bioinformatics, 2004