Statistical and computing resources offered by the Functional Genomics Lab

The Functional Genomics Lab offers statistical consulting services by the lab's Principal Statistician, Karen Vranizan ( ). Researchers involved at any stage of a microarray study are encouraged to take advantage of one hour of free consultation we offer per project. Additional services will be billed at $75.00 per hour on a recharge basis. We can provide any level of advice, training, or execution of the following technical services for either spotted array or Affymetrix platforms:

Microarray study design

simple and complex

Microarray data extraction and quality analysis

• Spot - spotted array gene expression quantification program using sophisticated image analysis and spot detection algorithms
• GenePix - spotted array gene expression quantification and quality assessment software
• RMA - gene expression quantification software based on models simultaneously fitting multiple Affymertrix GeneChips
• Affy MAS5 - Affymetrix proprietary gene expression quantification and quality assessment software

Statistical analysis

significance testing, multiple testing adjustment, false discovery rates, time course analysis

Cluster analysis

• Hierarchical Clustering - clustering method to detect order among genes (or array samples) and create trees based on pair-wise similarity between genes
• K-means - assignment of genes (or array samples) into k clusters of nearest neighbors
• HOPACH - hybrid clustering method, hierarchical ordered partitioning and collapsing hybrid (HOPACH), which is a hierarchical tree of clusters
• SOM - self-organizing maps, partitions genes into groups with similar expression patterns

Pathways and Gene Ontology

• GenMAPP - software to visualize gene expression data on metabolic and Gene Ontology maps

Statistical programming

• Bioconductor - an open source suite of microarray analysis programs for both spotted array and Affymetrix GeneChip experiments
• R
• SAS

Data Storage, Database

• GeneTraffic - web-based database to house and analyze microarray data of both spotted and Affymetrix types

Statistical interpretation and writing

Computer system resources offered by the Functional Genomics Lab

The FGL supports a Windows 2003 Server and Domain. Users are given a personal password-protected account on the FGL domain. Data and desktop are securely stored on the server and are accessible by any user logging onto the domain from any of our four public computers in the FGL. The server is firewalled and protected by nightly backup. One computer is reserved for scanner and GenePix users. The other three have all software necessary to do microarray analyses and standard Microsoft Office applications.

The FGL supports Gene Traffic, a web-based microarray database and analysis server. From any computer with Internet Explorer and an internet connection, a user can upload image and/or quantification files to the Gene Traffic server into a permanent project dataset. Data projects are linked to visualization, statistical, clustering tools, and extensive gene annotation, providing biologists easy discovery of differentially expressed genes and their biological connections. For a nominal fee, registered users are entitled to unlimited access to the Gene Traffic server, training, and support. Please contact Karen Vranizan for current recharge rates.