make.groups? And then heatmap.bin

Hello again.

I have a new doubt.

I have all my dataset in several files. After making some analyses I have this same number of .list files.
My problem is that I need to merge them into only one file to create some groups and finally to make a heatmap.

It would be possible to merge all these files with any mark to identify them in order to run make.groups? What kind of distinctive mark have they have to construct groups correctly?