Bioinformatics Toolbox™

getgeodata - Retrieve Gene Expression Omnibus (GEO) SOFT format data

Syntax

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

Arguments

`AccessionNumber`	String specifying a unique identifier for a GEO SOFT Sample (GSM) or Data Set (GDS) 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

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

Description

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

Field	Description
`Scope`	Type of data retrieved (SAMPLE or DATASET)
`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 Bioinformatics Toolbox™ software supports only Sample (GSM) and Data Set (GDS) 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.

For more information, see

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

Examples