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Data Import and Management

Import data and annotations from Affymetrix® GeneChip®, Illumina®, Agilent®, Gene Expression Omnibus (GEO), ImaGene®, SPOT, GenePix® GPR, and GAL; manage experimental data and sample metadata per MIAME standard

Functions

affyread Read microarray data from Affymetrix GeneChip file
affysnpannotread Read Affymetrix Mapping DNA array data from CSV-format annotation file
affyprobeseqread Read data file containing probe sequence information for Affymetrix GeneChip array
celintensityread Read probe intensities from Affymetrix CEL files
getgeodata Retrieve Gene Expression Omnibus (GEO) format data
geoseriesread Read Gene Expression Omnibus (GEO) Series (GSE) format data
geosoftread Read Gene Expression Omnibus (GEO) SOFT format data
galread Read microarray data from GenePix array list file
gprread Read microarray data from GenePix Results (GPR) file
agferead Read Agilent Feature Extraction Software file
ilmnbsread Read gene expression data exported from Illumina BeadStudio software
imageneread Read microarray data from ImaGene Results file
sptread Read data from SPOT file
goannotread Read annotations from Gene Ontology annotated file
cytobandread Read cytogenetic banding information

Classes

bioma.ExpressionSet Contain data from microarray gene expression experiment
bioma.data.ExptData Contain data values from microarray experiment
bioma.data.MetaData Contain metadata from microarray experiment
bioma.data.MIAME Contain experiment information from microarray gene expression experiment
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