Software Tutorials Available At AMC

 

The following tutorials are available upon request from AMC:

  • AMC Data Overview Presentation – General review of Affymetrix technology, file formats, algorithms, and AMC data preparation and quality assessment process.
  • Partek – Commercial microarray analysis software available for remote access and from the Bioinformatics Suite. Partek is unique in that it is relatively memory efficient and allows the User to analyze data from single or multiple array platforms simultaneously. This flexible and workflow-driven application offers interactive PCA analysis for QA/QC and multiple statistical options, including multi-factor, unbalanced analysis designs. Partek is compatible with Affymetrix 3’ IVT, Gene ST, Exon, SNP association studies, chromosomal copy number, promoter tiling array analysis, more (contact the AMC for more specifics). The recent update also includes a gene ontology browser. AMC grants investigators two-week access periods on a first-come, first-served basis.
  • GeneSifter –Web-based commercial microarray analysis software. Offers RMA, statistical analysis, Gene Ontology and Pathway reports, and various clustering and pattern search options. AMC grants investigators two-week access periods on a first-come, first-served basis.
  • MetaCore – a Web-based commercial pathway analysis and biological annotation database. MetaCore annotation is specific for human, rat, mouse; ortholog data is available for numerous other organisms.
  • TRANSFAC – Database of transcription factors, TF binding sites, gene regulators. Access granted is not time-sensitive (in person support not available).
  • Microsoft Excel – spreadsheet application, capable of data sorting and filtering.
  • Statistica – sophisticated statistical analysis software.
  • NetAffx – Affymetrix website used by investigators to update array annotation. Annotation included in NetAffx is updated on a quarterly basis.
  • GCOS – Affymetrix software that applies MAS5 alogrithm to generate signal values, detection calls and do pairwise comparisons.

If you'd like to schedule software access and/or a tutorial session, please contact Michelle Garred of the AMC at garredm@ohsu.edu .