dChip calls R for Linear discriminant analysis and the R dialog. To use them, install the R and R-COM software as below. This is optional and skipping the following steps will not affect other functions of dChip.

Installation of R and R-COM software

dChip can interface with R (http://www.r-project.org/, Ihaka and Gentleman 1996, JCGS), a statistical computing environment and language. R-COM (Neuwirth and Baier 2001) is a interface software to let R be used by other software such as Excel. Follow these steps to install the R and R-COM software:

· Install R. This interface does not work with the latest R. Please install R 2.3.1 or R 1.6.2 instead. At the “Select Components” dialog you may only select “main files”. Start R through “Start/Programs/R” to confirm R is installed properly; later on dChip will automatically start R. For R-COM to run properly, you may need to restart the computer after installing R to add registry key of R path to Windows.

· Install R-COM

[Before V12/14/07] : download and unzip R-COM binary files into a directory (can be the same directory as dchip.exe), and double-click setup.bat to setup R-COM. In dChip, check “Analysis/Open group/Options/Show ‘R View’ icon”.

[V12/14/07+] Install R-COM (run RSrv250.exe). Use the dChip “View/R Codes” menu to open an “R codes” dialog for running codes, and the Analysis View will be used for R output.

The R view

Click the “R command” button in the left panel to activate the “R view”:

There is an R command box and R output box, so general R commands such as “plot(1:10)” can be typed in and run. Commands such as “rownames(object)” do not return anything, and one should use “print(rownames(object))” instead. Here are some R codes useable in the R command box.

The “Get expression” button will export all the expression values into an R matrix with the name same as the dChip group name (“puneet” in the picture below). Then several R commands can be used, for example, to generate pair-wise scatter-plots between arrays. Since R doesn’t allow a variable name starting with numbers (e.g. “20burn”), one needs to specify an alternative group name (e.g. burn20) at “Analysis/Open group” in such case.