Bioinformatics Toolbox

gprread

Read microarray data from a GenePix Results (GPR) file

Syntax

GPRData = gprread('File', 
                  'PropertyName', PropertyValue...)

gprread(..., 'CleanColNames', CleanColNameValue)

Arguments

`File`	GenePix Results formatted file (file extension `GPR`). Enter a filename or a path and filename.
`CleanColNames`	Property to control creating column names that MATLAB can use as variable names.

Description

GPRData = gprread('File', 'PropertyName', PropertyValue...) reads GenePix results data from File and creates a MATLAB structure GPRData with the following fields:

Header
Data
Blocks
Columns
Rows
Names
IDs
ColumnNames
Indices
Shape

gprread(..., 'CleanColNames', CleanColNamesValue). A GPR file may contain column names with spaces and some characters that MATLAB cannot use in MATLAB variable names. If CleanColNames is true, gprread 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 invalid for MATLAB variable names.

The field Indices of the structure contains MATLAB indices that can be used for plotting heat maps of the data.

For more details on the GPR format, see

http://www.axon.com/GN_GenePix_File_Formats.html

For a list of supported file format versions, see

http://www.axon.com/gn_GPR_Format_History.html

Sample data can be found at the following Web address. Save this file to your working directory to run the example below.

http://www.axon.com/genomics/Demo.gpr

GenePix is a registered trademark of Axon Instruments, Inc.

Examples

% Read in a sample GPR file and plot the median
% foreground intensity for the 635nm channel.
gprStruct = gprread('mouse_alpd.gpr')
maimage(gprStruct,'F635 Median');

% Alternatively, create a similar plot using
% more basic graphics commands.

f635Col = find(strcmp(gprStruct.ColumnNames,'F635 Median'));
F635Median = gprStruct.Data(:,f635Col);
 imagesc(F635Median(gprStruct.Indices));
colormap bone
colorbar

gprread

Syntax

Arguments

Description

Examples

See Also