getgeodata - Retrieve Gene Expression Omnibus (GEO) format data

Syntax

Input 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. Tip   Recently submitted data sets may not be available for immediate download. There can be a one- to two-day delay between an experiment being submitted to the GEO database and its availability on the FTP site. Tip   If you are unable to retrieve data for an accession number, increase your Java™ heap space: If you have MATLAB version 7.10 (R2010a) or later, see Java Heap Memory Preferences If you have MATLAB version 7.9 (R2009b) or earlier, see http://www.mathworks.com/support/solutions/data/1-18I2C.html

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 Folder.

Output Arguments

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

geoStruct = getgeodata('GSM1768')

See Also

geoseriesread | geosoftread | getgenbank | getgenpept

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