The following Bioconductor packages have been exposed as caGrid-enabled exemplars; detailed information on each package is available on the Bioconductor web site. The services will be available at http://cabig.bioconductor.org/wsrf/. A snapshot of the underlying package code is available on the caBIG GForge site.
caAffy
The package contains functions for exploratory oligonucleotide array analysis.
Functionality includes background correction, normalization, and expression summaries.
Inputs are typically collections of microarray expression values representing data collected from several samples in a single experiment.
Outputs are typically transformed expression values or summary presentations. The MAGE-OM is used where possible.
caPROcess
PROcess is package for processing protein mass spectrometry data.
Functionality includes baseline subtraction, peak identification, and quality control.
Inputs are typically collections of SELDI-TOF mass spec scans representing data from a single experiment.
Outputs are typically transoformed scans, peak identification vectors, or summary presentations. The mzXML domain model is used where possible.
caDNAcopy
DNAcopy segments DNA copy number data collected from array CGH experiments, using circular binary segmentation to detect regions with abnormal copy number.
Functionality includes smothing and segmentating copy number data.
Typical inputs are vectors correspoonding to marker location and sample copy numbers.
Outputs are vectors of sample identifiers, segment start and stop positions, and related statistics.