Microarray Data Analysis
Contact: Jeff Delrow
Contact phone: (206) 667-2714
The Genomics Shared Resource provides access to HutchBASE, a customized version of BASE v2.6 (BioArray Software Environment) that was originally developed at Lund University in Sweden. BASE is an open-source, MIAME compliant, comprehensive web-based data storage and handling solution with additional LIMS capabilities. HutchBASE is used for sample submission, order processing, and workflow tracking, as well as data QC, pre-processing, and normalization. The application also allows for data interfacing with a number of downstream analysis applications.
Data analysis and annotation tools provided by the Resource include commercial software (e.g., Partek Genomics Suite, Ingenuity Pathway Analysis), as well as open-source software such as SAM, Cluster/TreeView, CyberT, FatiGO, Bioconductor packages (e.g., limma), MeV, etc. Data management and analysis tools are available to researchers through an IP-restricted website (http://genomics.fhcrc.org/). This website includes software downloads/connectivity instructions, instructional and training documents, and supporting files relevant to each application.
The Resource offers researchers personalized instruction in the use of various software tools, as well as consultation on data analysis concepts.