Documentation

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

Topics

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.

Exchange Bioinformatics Data Between Excel and MATLAB

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

Microarray Data Storage

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

Data Formats and Databases

Access online databases and repositories using various MATLAB^® functions and import data to the workspace for further analyses.

Featured Examples

Working with Affymetrix® Data

Working with Affymetrix® Data

Use the functions in the Bioinformatics Toolbox™ for working with Affymetrix® GeneChip® data.

Working with GEO Series Data

Working with GEO Series Data

Retrieve gene expression data series (GSE) from the NCBI Gene Expression Omnibus (GEO) and perform basic analysis on the expression profiles.

Bioinformatics Toolbox Documentation

Support