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# Features
- [Screenshots](<%=pathTo('/screenshots')%>)
- [Demos](<%=pathTo('/demos')%>)
- [Reproducible research](<%=pathTo('/replication')%>)
- [Limitations](<%=pathTo('/limitations/')%>)
- [Future directions](<%=pathTo('/features/future/')%>)
**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.
* 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)
* 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.
* 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.