geoseriesread

Read Gene Expression Omnibus (GEO) Series (GSE) format data

Syntax

GEOData = geoseriesread(File)
GEOData = geoseriesread(File,'TimeOut',TimeOutValue)

Input Arguments

File

Either of the following:

  • Character vector or 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) Series (GSE) format file. If you specify only a file name, that file must be on the MATLAB® search path or in the MATLAB current folder.

  • Character array or column vector of strings that contains the text of a GEO Series (GSE) format file.

Tip

You can use the getgeodata function with the 'ToFile' property to retrieve GEO Series (GSE) format data from the GEO database and create a GEO Series (GSE) format file.

TimeOutValueConnection timeout in seconds, specified as a positive scalar. The default value is 5. For details, see here.

Output Arguments

GEOData

MATLAB structure containing the following fields:

  • Header — Header text from the GEO Series (GSE) format file, typically containing a description of the data or experiment information.

  • Data — DataMatrix object containing the data from a GEO Series (GSE) format file. The columns and rows of the DataMatrix object correspond to the sample IDs and Ref IDs, respectively, from the GEO Series (GSE) format file.

Description

GEOData = geoseriesread(File) reads a Gene Expression Omnibus (GEO) Series (GSE) format file, and then creates a MATLAB structure, GEOData, with the following fields.

FieldsDescription
HeaderHeader text from the GEO Series (GSE) format file, typically containing a description of the data or experiment information.
DataDataMatrix object containing the data from a GEO Series (GSE) format file. The columns and rows of the DataMatrix object correspond to the sample IDs and Ref IDs, respectively, from the GEO Series (GSE) format file.

GEOData = geoseriesread(File,'TimeOut',TimeOutValue) sets the connection timeout (in seconds) to read data from a remote file or URL.

Examples

  1. Retrieve Series (GSE) data from the GEO Web site and save it to a file.

    geodata = getgeodata('GSE11287','ToFile','GSE11287.txt');

  2. In a subsequent MATLAB session, you can access the Series (GSE) data from your local file, instead of retrieving it from the GEO Web site.

    geodata = geoseriesread('GSE11287.txt')

geodata = 

    Header: [1x1 struct]
      Data: [45101x6 bioma.data.DataMatrix]

  3. Access the sample IDs using the colnames property of a DataMatrix object. 

    sampleIDs = geodata.Data.colnames

sampleIDs = 

  'GSM284935'  'GSM284936'  'GSM284937'  'GSM284938'  'GSM284939'  'GSM284940'

See Also

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Topics

Introduced in R2008b

Bioinformatics Toolbox Documentation

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