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. 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. |
|
| 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
geoStruct = getgeodata('GSM1768')
See Also
Bioinformatics Toolbox functions: geoseriesread, geosoftread, getgenbank, getgenpept
 | getgenpept | | gethmmalignment |  |
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