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imageneread

Read microarray data from ImaGene Results file

Syntax

imagenedata = imageneread('File')

imagenedata = imageneread(..., 'CleanColNames', CleanColNamesValue, ...)

Arguments

FileImaGene® Results formatted file. Enter a file name or a path and file name.
CleanColNamesValueControls the conversion of any ColumnNames containing spaces or characters that cannot be used as MATLAB® variable names, to valid MATLAB variable names. Choices are true or false (default).

Description

imagenedata = imageneread('File') reads ImaGene results data from File and creates imagenedata, a MATLAB structure containing the following fields.

Field
HeaderAA
Data
Blocks
Rows
Columns
Fields
IDs
ColumnNames
Indices
Shape

imagenedata = imageneread(..., 'PropertyName', PropertyValue, ...) calls imageneread with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:


imagenedata = imageneread(..., 'CleanColNames', CleanColNamesValue, ...)
controls the conversion of any ColumnNames containing spaces or characters that cannot be used as MATLAB variable names, to valid MATLAB variable names. Choices are true or false (default).

The field Indices of the structure contains indices that you can use for plotting heat maps of the data with the function image or imagesc.

For more details on the ImaGene format and example data, see the ImaGene documentation.

Examples

In the following example, the file cy3.txt is not provided.

  1. Read in a sample ImaGene Results file. Note that the example file, cy3.txt, is not provided with the Bioinformatics Toolbox™ software.

    cy3Data = imageneread('cy3.txt');
  2. Plot the signal mean.

    maimage(cy3Data,'Signal Mean');
  3. Read in a sample ImaGene Results file. Note that the example file, cy5.txt, is not provided with the Bioinformatics Toolbox software.

    cy5Data = imageneread('cy5.txt');
  4. Create a loglog plot of the signal median from two ImaGene Results files.

    sigMedianCol = find(strcmp('Signal Median',cy3Data.ColumnNames));
    cy3Median = cy3Data.Data(:,sigMedianCol);
    cy5Median = cy5Data.Data(:,sigMedianCol);
    maloglog(cy3Median,cy5Median,'title','Signal Median');

See Also

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