getgeodata

R2026b

Retrieve Gene Expression Omnibus (GEO) format data

Syntax

GEOData = getgeodata(AccessionNumber)

GEOData = getgeodata(AccessionNumber,Name=Value)

Description

GEOData = getgeodata(AccessionNumber) retrieves Gene Expression Omnibus (GEO) format data for the specified accession number of a Sample (GSM), Data Set (GDS), Platform (GPL), or Series (GSE) record.

GEOData = getgeodata(AccessionNumber,Name=Value) retrieves GEO data with additional options specified by one or more name-value arguments. For example, you can save the data to a file or set a connection timeout.

Examples

Get GEO Data

Retrieve GEO data for accession number GSM1768.

GEOdata = getgeodata("GSM1768")

GEOdata = 

  struct with fields:

                 Scope: 'SAMPLE'
             Accession: 'GSM1768'
                Header: [1×1 struct]
    ColumnDescriptions: {3×1 cell}
           ColumnNames: {3×1 cell}
                  Data: {1656×3 cell}

Input Arguments

AccessionNumber — GEO record accession number

character vector | string scalar

GEO record accession number, specified as a character vector or string scalar. The accession number is 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

• 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.

• 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 Runtime Environment Settings.

  • 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.

Data Types: char | string

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: GEOdata = getgeodata("GSM1768",ToFile="GSM1768.txt") specifies to save the results to a file.

ToFile — Output file name

character vector | string scalar

Output file name, specified as a character vector or string scalar. If you specify only a file name, that file is saved in the MATLAB current folder.

Data Types: char | string

TimeOut — Connection timeout

5 (default) | positive scalar

Connection timeout, specified as a positive scalar in seconds. For details, see here.

Data Types: double

Output Arguments

GEOData — GEO record data

structure

GEO record data, returned as a 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.

Version History

Introduced before R2006a