Bioinformatics Toolbox™

geosoftread - Read Gene Expression Omnibus (GEO) SOFT format data

Syntax

GEOSOFTData = geosoftread(File)

Arguments

File

Either of the following:

String specifying a file name, a path and file name, or a URL pointing to a file. The referenced file is a Gene Expression Omnibus (GEO) SOFT format Sample file (GSM) or Data Set file (GDS). If you specify only a file name, that file must be on the MATLAB^® search path or in the current directory.
MATLAB character array that contains the text of a GEO SOFT format file.

Tip You can use the getgeodata function with the 'ToFile' property to retrieve GEO SOFT format data from the GEO database and create a GEO SOFT format file.

Return Values

GEOSOFTData MATLAB structure containing information from a GEO SOFT format file.

Description

GEOSOFTData = geosoftread(File) reads a Gene Expression Omnibus (GEO) SOFT format Sample file (GSM) or Data Set file (GDS), and then creates a MATLAB structure, GEOSOFTdata, with the following fields.

Fields	Description
`Scope`	Type of file read (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.

Examples

Retrieve GSM data from the GEO Web site and save it to a file.

geodata = getgeodata('GSM3258','ToFile','GSM3258.txt');

Use geosoftread to read a local copy of the GSM file, instead of accessing it from the GEO Web site.

geodata = geosoftread('GSM3258.txt')

geodata = 

                 Scope: 'SAMPLE'
             Accession: 'GSM3258'
                Header: [1x1 struct]
    ColumnDescriptions: {6x1 cell}
           ColumnNames: {6x1 cell}
                  Data: {5355x6 cell}

Read the GDS file for photosynthesis in proteobacteria.