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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

affyreadRead microarray data from Affymetrix GeneChip file
affysnpannotreadRead Affymetrix Mapping DNA array data from CSV-format annotation file
affyprobeseqreadRead data file containing probe sequence information for Affymetrix GeneChip array
celintensityreadRead probe intensities from Affymetrix CEL files
getgeodataRetrieve Gene Expression Omnibus (GEO) format data
geoseriesreadRead Gene Expression Omnibus (GEO) Series (GSE) format data
geosoftreadRead Gene Expression Omnibus (GEO) SOFT format data
galreadRead microarray data from GenePix array list file
gprreadRead microarray data from GenePix Results (GPR) file
agfereadRead Agilent Feature Extraction Software file
ilmnbsreadRead gene expression data exported from Illumina BeadStudio software
imagenereadRead microarray data from ImaGene Results file
sptreadRead data from SPOT file
goannotreadRead annotations from Gene Ontology annotated file
cytobandreadRead cytogenetic banding information

Classes

bioma.ExpressionSetContain data from microarray gene expression experiment
bioma.data.ExptDataContain data values from microarray experiment
bioma.data.MetaDataContain metadata from microarray experiment
bioma.data.MIAMEContain 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

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

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