Data Preparation

Generating the raw image is not the end of the microarray service in the Affymetrix Microarray Core.  Data Preparation for Expression Projects with the Affymetrix Microarray Core consists of:

  • Preparation of a Project Report, summarizing sample processing and array assay performance.
  • The "Genome Report Summary," a spreadsheet of metrics associated with quality and control information.  This sheet is color-coded to reflect any outlier or otherwise flagged metrics.
  • Data visualization plots, including Box Plots and Scatter Plots of unscaled, summarized data.  These are prepared so that User's can immediately assess the overall data distribution and correlation for project sample data.
  • Text files (.txt) of unscaled and scaled data, prepared using the Affymetrix MAS 5.0 algorithm.  These text files may be opened in Excel for immediate filtering/sorting.  Note: these files include design-time gene descriptions; the NetAffx tool may be used to update gene annotation.
  • All raw, processed, and quality assessment (QA) data resulting from array hybridization are shipped on DVD/CD to the investigator's lab. 
  • One-on-one tutorial options including array design/annotation descriptions, array assay overview, MAS 5.0 algorithm overview, introductory navigation of core-licensed data analysis software, MIAME publication guidelines, uploading data to an online public repository.