Data Import and Management
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.