Using Spreadsheet Link EX with Bioinformatic Data :: Getting Started (Bioinformatics Toolbox™)

Using Spreadsheet Link EX with Bioinformatic Data

If you have bioinformatic data in a Microsoft Excel spreadsheet, you can use Spreadsheet Link EX software to connect Excel with the MATLAB Workspace to exchange data and to 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 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 has been filtered using the steps described in the Gene Expression Profile Analysis demo.

If you have not already done so, modify your system path to include the MATLAB root directory as described in Modifying Your System Path in the Spreadsheet Link EX documentation.
If you have not already done so, configure the software as described in Configuring the Spreadsheet Link EX Software in the Spreadsheet Link EX documentation.
Close MATLAB if you have it open.
Start Microsoft Excel. MATLAB and Spreadsheet Link EX software open also.
From Excel, open the following file provided with the Bioinformatics Toolbox software:
```
matlabroot\toolbox\bioinfo\biodemos\Filtered_Yeastdata.xls
```
Note that cells J5, J6, J7, and J12 of the spreadsheet contain formulas using Spreadsheet Link EX functions MLPutMatrix and MLEvalString.
Cells J5, J6, and J7 each create a MATLAB variable from the data in the spreadsheet, and cell J12 runs the Bioinformatics Toolbox clustergram function using these three variables as input. For more information on adding formulas using Spreadsheet Link EX functions, see Entering Functions into Worksheet Cells in the Spreadsheet Link EX documentation.

Note that cell J17 contains a formula using a macro function 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. To view the Clustergram macro function, select Tools > Macro > Visual Basic Editor. For more information on creating macros using Visual Basic Editor, see Examples: Using Spreadsheet Link EX Functions in Macros in the Spreadsheet Link EX documentation.
Run the formula in cell J17 to analyze and visualize the data:
1. Select cell J17.
2. Press F2.
3. Press Enter.
The macro function Clustergram runs creating three MATLAB variables (data, Genes, and 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:
1. Select cell J5, then press F2 to display the formula for editing. Change H617 to H33, then press Enter.
2. Select cell J6, then press F2 to display the formula for editing. Change A617 to A33, then press Enter.
Run the formulas in cells J5, J6, J7, and J12 to analyze and visualize a subset of the data.
1. Select cell J5, press F2, then press Enter.
2. Select cell J6, press F2, then press Enter.
3. Select cell J7, press F2, then press Enter.
4. Select cell J12, press F2, then press Enter.
Use the commands in the Spreadsheet Link EX toolbar to interact with the data:
1. Click-drag to select cells B5 through H7, click putmatrix in the toolbar, type YAGenes for the variable name, then click OK. The variable YAGenes is added to the MATLAB Workspace as a 3-by-7 matrix.
2. Click evalstring in the toolbar, type plot(YAGenes') for the command, then click OK. A Figure window displays a plot of the data.
3. Select cell J20, then click getfigure in the toolbar. The figure is added to the spreadsheet