If you have bioinformatics data in an Excel® (2007 or 2010) spreadsheet, use Spreadsheet Link™ EX to:
Connect Excel with the MATLAB® Workspace to exchange data
Use MATLAB and Bioinformatics Toolbox™ computational and visualization functions
Note: The following example assumes you have Spreadsheet Link EX software installed on your system.
The Excel file used in the following example contains data from DeRisi, J.L., Iyer, V.R., and Brown, P.O. (Oct. 24, 1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278(5338), 680–686. PMID: 9381177. The data was filtered using the steps described in Gene Expression Profile Analysis.
If not already done, modify your system path to include the MATLAB root folder as described in the Spreadsheet Link EX documentation.
If not already done, enable the Spreadsheet Link EX Add-In as described in Set Spreadsheet Link EX Preferences and MATLAB Version in the Spreadsheet Link EX documentation.
Close MATLAB and Excel if they are open.
Start Excel 2007 or 2010 software. MATLAB and Spreadsheet Link EX software automatically start.
From Excel, open the following file provided with the Bioinformatics Toolbox software:
In the Excel software, enable macros. Click the Developer tab, and then select Macro Security from the Code group. (If the Developer tab is not displayed on the Excel ribbon, consult Excel Help to display it.)
In the provided Excel file, note that columns
A through H contain data from DeRisi et al. Also note that cells J5,
J6, J7, and J12 contain formulas using Spreadsheet Link EX functions
Tip To view a cell's formula, select the cell, and then view the formula in the formula bar at the top of the Excel window.
Execute the formulas in cells J5, J6, J7, and J12, by selecting the cell, pressing F2, and then pressing Enter.
Each of the first three cells contains a formula using the Spreadsheet Link EX function
which creates a MATLAB variable from the data in the spreadsheet.
Cell J12 contains a formula using the Spreadsheet Link EX function
which runs the Bioinformatics Toolbox
using the three variables as input. For more information on adding
formulas using Spreadsheet Link EX functions, see Enter Functions into Worksheet Cells in the Spreadsheet Link EX documentation.
Note that cell J17 contains a formula using a macro
Clustergram, which was created in the Visual Basic® Editor.
Running this macro does the same as the formulas in cells J5, J6,
J7, and J12. Optionally, view the
function by clicking the Developer tab, and then
clicking the Visual Basic button
. (If the Developer tab
is not on the Excel ribbon, consult Excel Help to display it.)
For more information on creating macros using Visual Basic Editor, see Use Spreadsheet Link EX Functions in Macros in the Spreadsheet Link EX documentation.
Execute the formula in cell J17 to analyze and visualize the data:
Select cell J17.
The macro function
Clustergram runs creating
three MATLAB variables (
TimeSteps) and displaying a Clustergram window
containing dendrograms and a heat map of the data.
Edit the formulas in cells J5 and J6 to analyze a subset of the data. Do this by editing the formulas' cell ranges to include data for only the first 30 genes:
Select cell J5, and then press F2 to display the formula for editing. Change H617 to H33, and then press Enter.
Select cell J6, then press F2 to display the formula for editing. Change A617 to A33, and then press Enter.
Run the formulas in cells J5, J6, J7, and J12 to analyze and visualize a subset of the data:
Select cell J5, press F2, and then press Enter.
Select cell J6, press F2, and then press Enter.
Select cell J7, press F2, and then press Enter.
Select cell J12, press F2, and then press Enter.
Use the MATLAB group on the right side of the Home tab to interact with the data:
For example, create a variable in MATLAB containing a 3-by-7 matrix of the data, plot the data in a Figure window, and then add the plot to your spreadsheet:
Click-drag to select cells B5 through H7.
From the MATLAB group, select Send data to MATLAB.
Type YAGenes for the variable name, and then click OK.
The variable YAGenes is added to the MATLAB Workspace as a 3-by-7 matrix.
From the MATLAB group, select Run MATLAB command.
the command, and then click OK.
A Figure window displays a plot of the data.
Make sure you use the
Select cell J20, and then click from the MATLAB group, select Get MATLAB figure.
The figure is added to the spreadsheet.