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Last update: 22/02/10 

 

 

Genomic analysis

Overview

The Genomics Data Analysis units offers "full-service" bioinformatics analyses of microarray-generated data. We provide on-site user support, conduct tutorials and workshops on microarray data analysis, and provide comprehensive data management and analysis.

Services

Specific services include, but are not limited to:

  • Consultation on experimental design
  • General statistical consulting
  • Data management and preparation (e.g., pre-processing)
  • Custom software design and development
  • Biostatistics and bioinformatics support for all types of microarray platforms: two-color cDNA, one-color and two-color oligonucleotide, Affymetrix
  • Microarray data normalization and identification of differentially expressed genes
  • Microarray data visualization and exploratory analysis (e.g., clustering)
  • Data analysis, interpretation, and report preparation
  • Assistance on grant or protocol submission (e.g., preparing statistical analysis plan or database description)
  • Manuscript review and preparation
  • Advanced training on microarray analysis

Tools

To facilitate effective analysis of microarray data we are using both commercial , free available packages and additional custom built packages as needed by the researchers.

  • A dedicated custom built server (Matlab and Perl Based) to assist in quality assurance, calibration and data normalization (Lowes) on line for GPR files generated in our microarray lab facility.
  • Special filters and other built image processing packages to handle image scanning problems.
  • Statistical analysis, data normalization and clustering are carried out with several software packages: Spotfire, Acuity, Jsota,Genepix, ScanAyze,SAM (for multiple comparisons).
  • Custom packages build using Matlab and Perl.
  • Access to free available packages such as Bioconductor or Afymetrix and other gene annotation tools.
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