affy

The software tool "affy," specifically through its program Pigeons, is designed to facilitate the analysis of genomic and transcriptomic data from heterologous species using high-density oligonucleotide arrays. It addresses the lack of a user-friendly graphical interface for parsing oligonucleotide probe pair-level data in cross-species experiments. Pigeons allow users to import and analyze Affymetrix GeneChip® probe level data, determine empirical boundaries to remove poor probes, and create species-specific Chip Description File (CDF) for transcriptomics in non-model or underutilized species. It also aids in examining experimental designs to identify potential Single-Feature Polymorphisms (SFPs) at DNA or RNA levels.

Topic

Gene expression;Data mining;Data visualisation

Detail

  • Operation: Gene expression analysis

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: GNU Lesser General Public License >=v2

  • Cost: Free

  • Version name: 1.74.0

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Rafael A. Irizarry rafa@jhu.edu, Rafael A. Irizarry rafa@ds.harvard.edu

  • Collection: Bioconductor

  • Maturity: -

Publications

  • affy--analysis of Affymetrix GeneChip data at the probe level
  • Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004 Feb 12;20(3):307-15. doi: 10.1093/bioinformatics/btg405. PMID: 14960456.
  • https://doi.org/10.1093/bioinformatics/btg405
  • PMID: 14960456
  • PMC: -

Download and documentation

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