Bioinformatics Toolbox™

imageneread - Read microarray data from ImaGene^® Results file

Syntax

imagenedata = imageneread('File')

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

Arguments

Description

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

imagenedata = imageneread(..., 'PropertyName', PropertyValue, ...) defines optional properties using property name/value pairs, described as follows:

imagenedata = imageneread(..., 'CleanColNames', CleanColNamesValue, ...). An ImaGene file may contain column names with spaces and some characters that the MATLAB software cannot use in MATLAB variable names. If CleanColNamesValue is true, imagene returns, in the field ColumnNames, names that are valid MATLAB variable names and names that you can use in functions. By default, CleanColNamesValue is false and the field ColumnNames may contain characters that are not valid for MATLAB variable names.

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 User Manual.

Examples

1. Read in a sample ImaGene Results file. Note, the 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, the 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

Bioinformatics Toolbox functions: gprread, ilmnbsread, maboxplot, maimage, sptread

ilmnbsread

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