oligo-package: The oligo package: a tool for low-level analysis of...
In benilton/oligoOld: Preprocessing tools for oligonucleotide arrays

Description Details Author(s) References

The oligo package provides tools to preprocess different oligonucleotide arrays types: expression, tiling, SNP and exon chips. The supported manufacturers are Affymetrix and NimbleGen.

It offers support to large datasets (when the bigmemory is loaded) and can execute preprocessing tasks in parallel (if, in addition to bigmemory, the snow package is also loaded).

The package will read the raw intensity files (CEL for Affymetrix; XYS for NimbleGen) and allow the user to perform analyses starting at the feature-level.

Reading in the intensity files require the existence of data packages that contain the chip specific information (X/Y coordinates; feature types; sequence). These data packages packages are built using the pdInfoBuilder package.

For Affymetrix SNP arrays, users are asked to download the already built annotation packages from BioConductor. This is because these packages contain metadata that are not automatically created. The following annotation packages are available:

50K Xba - pd.mapping50kxba.240 50K Hind - pd.mapping50khind.240 250K Sty - pd.mapping250k.sty 250K Nsp - pd.mapping250k.nsp GenomeWideSnp 5 (SNP 5.0) - pd.genomewidesnp.5 GenomeWideSnp 6 (SNP 6.0) - pd.genomewidesnp.6

For users interested in genotype calls for SNP 5.0 and 6.0 arrays, we strongly recommend the use use the crlmm package, which implements a more efficient version of CRLMM.

Benilton Carvalho - carvalho@bclab.org

Carvalho, B.; Bengtsson, H.; Speed, T. P. & Irizarry, R. A. Exploration, Normalization, and Genotype Calls of High Density Oligonucleotide SNP Array Data. Biostatistics, 2006.

benilton/oligoOld documentation built on May 12, 2019, 11:52 a.m.