Features
MOVE THE BELOW TO SUBPAGE(S):
CHIP TYPES/DATA FILES:
- Number of arrays: unlimited.
- Chip types: all Affymetrix chip types with a CDF, e.g. SNP, exon,
and gene expression.
- Immediate support for custom CDFs, e.g. Brainarray and AffyProbeMiner.
- Chip types: all Affymetrix chip types with a CDF, e.g. SNP, exon,
and gene expression.
- File formats: Works directly with CEL and CDF files (all versions; text/ASCII, binary/XDA, binary/Calvin).
LOW-LEVEL ANALYSIS:
- Pre-processing: Background correction, allelic cross-talk
calibration, quantile normalization etc.
- Probe-level modeling: RMA (log-additive), MBEI (multiplicative),
affine (multiplicative with or without offset).
- Post-processing: PCR fragment-length normalization.
IMPORT/EXPORT:
- Export to/Import from: Bioconductor, CNAG, CNAT & dChip.
REPORTS:
- Dynamic HTML reports: ArrayExplorer (HapMap demo), ChromosomeExplorer (HapMap demo, Tumor/Normal demo). Requires Firefox.
DOCUMENTATION/HELP:
- Documentation: Online documentation is collected under Pages.
- Vignettes: Online example code is collected in Section Vignettes.
DESIGN/IMPLEMENTATION:
- Bounded-memory algorithms.
- Low memory requirements: Minimum 500MB RAM (recommended >1GB RAM)
- Low memory requirements: Minimum 500MB RAM (recommended >1GB RAM)
- Persistent data and result storage: Final and intermediate results
and estimates are stored on file.
- Robustness: Analysis picks up where last interrupted.
- Portable scripts: All data files are referred to by relative
pathnames.
- Robustness: Analysis picks up where last interrupted.
- Cross platform: Work with any operating system.
- Design goals: usability, quality & extendibility.
COPY-NUMBER ANALYSIS:
- Paired & non-paired copy-number analysis: All generations, i.e. 10K, 100K, 500K, 5.0 & 6.0. CBS & GLAD * segmentation methods. Combine data from multiple chip types.
EXON ARRAY ANALYSIS:
- Alternative splicing: FIRMA.
EXPRESSION AND MORE:
- Most Affymetrix chip types are supported.