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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

Examples and How To

Managing Gene Expression Data in Objects

Overview of objects for Microarray Gene Expression Data

Representing Expression Data Values in DataMatrix Objects

Construct DataMatrix objects, get and set properties, and access data.

Representing Expression Data Values in ExptData Objects

Construct ExptData objects, use properties and methods, and access data.

Representing Sample and Feature Metadata in MetaData Objects

Construct MetaData objects, use properties and methods, and access data.

Representing Experiment Information in a MIAME Object

Construct MIAME objects, use properties and methods, and access data.

Representing All Data in an ExpressionSet Object

Construct ExpressionSet objects, use properties and methods, and access data.

Visualizing Microarray Images

Create figures to visualize microarray data and get the data ready for analysis.

Exchange Bioinformatics Data Between Excel and MATLAB

Example of using Spreadsheet Link™ with software to view bioinformatic data

Concepts

Microarray Data Storage

The Bioinformatics Toolbox™ includes functions, objects, and methods for creating, storing, and accessing microarray data.

Data Formats and Databases

The Bioinformatics Toolbox accesses many of the databases on the Web and other online data sources.

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