Bioinformatics Toolbox™

getgeodata - Retrieve Gene Expression Omnibus (GEO) format data

Syntax

GEOData = getgeodata(AccessionNumber) getgeodata(AccessionNumber, 'ToFile', ToFileValue)

Arguments

`AccessionNumber`	String specifying a unique identifier for a GEO Sample (GSM), Data Set (GDS), Platform (GPL), or Series (GSE) record in the GEO database.
`ToFileValue`	String specifying a file name or path and file name for saving the data. If you specify only a file name, that file will be saved in the MATLAB Current Directory.

Return Values

GEOData MATLAB structure containing information for a GEO record retrieved from the GEO database.

Description

GEOData = getgeodata(AccessionNumber) searches the Gene Expression Omnibus database for the specified accession number of a Sample (GSM), Data Set (GDS), Platform (GPL), or Series (GSE) record and returns a MATLAB structure containing the following fields:

Field	Description
`Scope`	Type of data retrieved (SAMPLE, DATASET, PLATFORM, or SERIES)
`Accession`	Accession number for record in GEO database.
`Header`	Microarray experiment information.
`ColumnDescriptions`	Cell array containing descriptions of columns in the data.
`ColumnNames`	Cell array containing names of columns in the data.
`Data`	Array containing microarray data.
`Identifier` (GDS files only)	Cell array containing probe IDs.
`IDRef` (GDS files only)	Cell array containing indices to probes.

Note Currently, the getgeodata function supports Sample (GSM), Data Set (GDS), Platform (GPL), and Series (GSE) records.

getgeodata(AccessionNumber, 'ToFile', ToFileValue) saves the data returned from the database to a file.

Note You can read a GEO SOFT-formatted file back into the MATLAB software using the geosoftread function. You can read a GEO SERIES-formatted file back into the MATLAB software using the geoseriesread function.

For more information, see

http://www.ncbi.nlm.nih.gov/About/disclaimer.html

Examples