| Bioinformatics Toolbox | |
Read microarray data from an ImaGene Results file
GPRData = gprread('File',
'PropertyName', PropertyValue...)
gprread(..., 'CleanColNames', CleanColNamesValue)
File | ImaGene Results formatted file Enter a filename or a path and filename. |
CleanColName | Property to control creating column names that MATLAB can use as variable names. |
imagedata = imagegeenread(File, 'PropertyName', PropertyValue...) reads ImaGene results data from File and creates a MATLAB structure imagedata containing the following fields:
HeaderAA Data Blocks Rows Columns Fields IDs ColumnNames Indices Shape
imageneread(..., 'CleanColNames', CleanColNamesValue). An ImaGene file may contain column names with spaces and some characters that MATLAB cannot use in MATLAB variable names. If CleanColNames is true, imagene returns ColumnNames that are valid MATLAB variable names and names that you can use in functions. By default, CleanColNames is false and ColumnNames may contain characters that are not valid for MATLAB variable names.
The field Indices of the structure contains MATLAB indices that you can use for plotting heat maps of the data with the functions image or imagesc.
For more details on the ImaGene format and example data, see the ImaGene User Manual. .
ImaGene is a registered trademark of BioDiscovery, Inc.
% Read in a sample ImaGene file and plot the Signal Mean
cy3Data = imageneread('cy3.txt');
maimage(cy3Data,'Signal Mean');
% Read in the Cy5 channel and create a loglog plot of Signal Median
cy5Data = imageneread('cy5.txt');
sigMedianCol = find(strcmp('Signal Median',cy3Data.ColumnNames));
cy3Median = cy3Data.Data(:,sigMedianCol);
cy5Median = cy5Data.Data(:,sigMedianCol);
maloglog(cy3Median,cy5Median,'title','Signal Median');
The Bioinformatics Toolbox functions gprread, maboxplot, maimage, sptread
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