1) "Choose mask file" will show you File open dialog box for selecting mask file downloaded from this website.

2) "Choose CEL file" will show you File open dialog box for choosing the CEL file you want to modify. Instead of this, you can use "Choose directory" button, which opens dialog box for selecting a directory where a set of CEL files reside. In this case, all the CEL files in the chosen directory will be converted.

3) Before starting conversion, you may determine a suffix which will be put on output file name (i.e., the name of converted CEL file). It is for discriminating the original CEL file with the modified one. Just type a suffix name in Text box and then push "Set suffix" button. (Default is "_masked".)

We suggest that you will use the name of mask file as suffix. For example, if your mask file name is "U95Av2_FL_18_8.txt", you can use "_U95Av2_FL_18_8" as suffix. In this case, if your original CEL file name is "ExampleCEL.cel", the converted CEL file name will be "ExampleCEL_U95Av2_FL_18_8.cel".

4) Finally, you will start conversion process by pushing "Convert!" button. After conversion, a pop-up window tells you the number of converted CEL files.

5) You can analyze the converted CEL file using popular softwares such as MAS, dCHIP, and Bioconductor.