StAM - Structured Analysis of Microarrays

stam is an R/Bioconductor Package which implements our structured analysis of microarrays method. Thereby we link classification results to biologically focussed classifiers. The biological terms used are derived from the geneontology.org/Gene Ontology. For further information see the StAM project page

Publications

• stam - a Bioconductor compliant R package for structured analysis of microarray data
  Lottaz C and Spang R.
  BMC Bioinformatics, 2005, 6 (1): 211.
  [ pmid: 16122395 |  doi: 10.1186/1471-2105-6-211 ]
• Molecular Decomposition of Complex Clinical Phenotypes using Biologically Structured Analysis of Microarray Data
  Lottaz C and Spang R.
  Bioinformatics, 2005, 21 (9): 1971-1978.
  [ pmid: 15677704 |  doi: 10.1093/bioinformatics/bti292 ]
• Structured Analysis of Microarrays - User's Guide to the Bioconductor package StAM
  Lottaz C and Spang R.
  CompDiag Technical Report Nr. 2004/03 Nov. 2004
  [ pdf ]

Download

Download the package either as source or as windows binary . To run the package, you need R and at least packages Biobase, GO and annaffy from Bioconductor. Furthermore, meta data packages for all microarray platforms you want to analyze are needed. To run the examples, you also need the package golubEsets.

→ the released version
→ the development version