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# An open-source R framework for your microarray analysis
![FIRMA and alternative splicing](<%=pathTo('assets/images_thumbs/exon_array_example_plot.png')%>)
![Allelic crosstalk](<%=pathTo('assets/images_thumbs/NA06985_Hind_B5_3005533-allelicPairsAT.png')%>)
The aroma.affymetrix package is an R package for analyzing small to
extremely large Affymetrix data sets. It allows you to analyze any number
of arrays of various chip types, e.g. 10,000s of expression arrays, SNP chips,
exon arrays and so on.
Here are some of the features of aroma.affymetrix:
- Number of arrays: **unlimited**.
- System requirements: As low as **1 GiB RAM, any operating system**.
- **Parallel processing**: [Single setting](<%=pathTo('/howtos/parallel_processing')%>) to process data on multiple cores, in the background on multiple R sessions on the local machine, on a computer cluster etc.
- Chip types: **all Affymetrix** [chip types](<%=pathTo('/chipTypes/')%>) with a CDF, e.g. gene expression, exon, SNP & CN, tiling arrays.
- Immediate support for **custom CDFs**, e.g. [Brainarray](, [GeneAnnot]( and [Wageningen University-NuGO](
- File formats: Works directly with **CEL and CDF files** (all
versions; text/ASCII, binary/XDA, binary/Calvin).
- Export to/Import from: Bioconductor, CNAG, CNAT & dChip.
- Pre-processing: Background correction, allelic cross-talk
calibration, quantile normalization, nucleotide-position
normalization etc.
- Probe-level modeling: RMA (log-additive), MBEI (multiplicative),
affine (multiplicative with or without offset), ACNE (non-negative
matrix factorization).
- Post-processing: PCR fragment-length and/or GC-content
- Paired & non-paired copy-number analysis: All generations, including
10K, 100K, 500K, 5.0, 6.0, and CytoScanHD. Estimation of
full-resolution (raw) copy numbers using CRMA (10K-500K) and CRMAv2
(10K-CytoScanHD). Combine data from multiple chip types.
Segmentation methods such as CBS, GLAD and HaarSeg.
- Genotyping: CRLMM (100K & 500K).
- Alternative splicing: FIRMA.
- **Dynamic HTML reports**: [ArrayExplorer & ChromosomeExplorer](<%=pathTo('/demos/')%>).
- **Persistent memory**: Final and intermediate results and estimates
are stored on the file system.
- **Robustness**: Analysis picks up where last interrupted. Only
complete files are produced (even during power failures).
- Reproducibility: Near **perfect replication** of RMA, GCRMA and
SNPRMA (normalization & summarization) as implemented in the
affyPLM, affy, gcrma and oligo packages, as well as CRLMM
(genotyping) of oligo.
- **Portable scripts**: All data sets and data files are referred to
by their names - not by pathnames.
- Design goals: usability, quality & extendibility.