data prep and management
Data Preparation
Data Preparation includes the following steps:
- Visual inspection of all raw image scans
- Visualization of overall distribution and/or sample correlation by data plots of unscaled, non-normalized data
- Assessment of standard array quality metrics, which are output in Excel format
- Preparation of a Project Report, which includes assay processing details as well as a core project assessment, description of all output files, and a listing of core and external post-project support options
- All array data files are provided; scaled/normalized data files are also provided for expression projects
Data Management
The Affymetrix Microarray Core practices data redundancy for an increased level of data security. Within the core, raw array data files are maintained on a local drive and raw, processed, and quality assessment (QA) data is maintained in the disc archives. Also, all data that is delivered to the investigator's lab is transferred to a server that is maintained by OHSU's computing group, AGCC. These storage steps, along with the copy of data that is distributed directly to the investigator's lab offers a significant degree of data stability.
Note: The Affymetrix Microarray Core is not responsible for lost data post-project completion. The investigator's lab is encouraged to practice redundant back-up measures to protect against lost/corrupted data discs, drive failure, etc.
Data Security
Strict policies surround data security in the Affymetrix Microarray Core. Project correspondences and project data are released only to investigators that are listed on the Project Application and Sample Submission Form. A principal investigator may add/delete an investigator from the project forms by e-mailing Michelle Garred, Affymetrix Microarray Core/GMSR User Support (garredm@ohsu.edu).
