Software

Written by Ben Bolstad
email bmb@bmbolstad.com

What is here?

This page provides links and brief descriptions of various pieces of software I have written. Most of it is for the analysis of microarray data.

ProgramDescriptionWhere to get
RMAExpressA program for generating RMA expression values for Affymetrix GeneChip microarrays. Source code is available licensed under the GPL. Pre-compiled binaries are available for Microsoft operating systems. May also be built successfully on Linux operating systems. Consists of three separate programs: RMAExpress which is a GUI program, RMAExpressConsole runs on the command line and RMADataConv for certain file format conversions.rmaexpress.bmbolstad.com
affyAn R package for low-level analysis of Affymetrix GeneChip data. Provides some pre-processing facilities and methods for examining probe intensity data. Joint work with Rafael Irizarry, Laurent Gautier and others. Includes the R function rma() for computing RMA expression values and also the base implementation of the quantile normalization algorithm.www.bioconductor.org
affyPLMAn R package providing methods for fitting probe-level models to Affymetrix GeneChip data. Provides additional pre-processing methods beyond those in the base affy package. It provides quality assessment tools for GeneChip data such as the figures at PLMImageGallery.bmbolstad.com.www.bioconductor.org
affyioThis R package provides parsers for Affymetrix file formats based upon available documentation.www.bioconductor.org
AffyExtensionsAn R package which provides additional, but sometimes experimental, functionality for the analyzing Affymetrix data. Has often served as a place where functionality is developed that is later moved into the affy and affyPLM packages. Because of possible instability (although usually everything is fine) this remains outside BioConductor although it supplements and depends on many of these packages.AffyExtensions
BufferedMatrixThis is an experimental R package which implements an out of memory matrix for dealing with large datasets, Buffers are used to provide some level of speed up. Currently sources are stored in the BioC svn archive. Some simulation results are here.BioConductor svn repository (user: readonly, pass: readonly)
BufferedMatrixMethodsThis is an experimental R package which uses the BufferedMatrix structures for microarray processing. Some simulation results are here.BioConductor svn repository (user: readonly, pass: readonly)
preprocessCoreThis R package contains a number of low-level preprocessing routines. The interface to this code is both at the C-level and the R-level. Both affy and affyPLM depend on this package. You can find a discussion of runtime performance of the PLM fitting code here. Other simulation/testing results for preprocessCore are stored here.www.bioconductor.org
SMA Statistics for Microarray Analysis (SMA) was an early R package for pre-processing/normalization of cDNA and other two color microarray data. At this point (Jul 2006) it is mostly defunct and has been superceded by software in BioConductor. This package was joint work with Sandrine Dudoit and Jean Yang.SMA webpage
Also see CRAN

Questions?

Send me an email at bmb@bmbolstad.com.