getgeodata

Retrieve Gene Expression Omnibus (GEO) format data

Syntax

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


Input Arguments

AccessionNumber	Character vector specifying a unique identifier for a GEO Sample (GSM), Data Set (GDS), Platform (GPL), or Series (GSE) record in the GEO database. Next-Generation Sequencing data cannot be retrieved using this function. 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 https://www.mathworks.com/matlabcentral/answers/92813-how-do-i-increase-the-heap-space-for-the-java-vm-in-matlab. 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.
ToFileValue	Character vector 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.
TimeOutValue	Connection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.

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

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

GEOData = getgeodata(AccessionNumber,'TimeOut',TimeOutValue) sets the connection timeout (in seconds) to retrieve data from the Gene Expression Omnibus database.

Examples

geoStruct = getgeodata('GSM1768')

Version History

Introduced before R2006a