Demosaicing with dcraw, as suggested, is one way around a lack of demosaicing support for RAF files with some preprocessing programs.
v9.19 available with Ubuntu converts RAF and there are Windows executables available for download here and there.
MacOS Yosemite has support as well, though not sure which version of dcraw.
Here if you are a Windows user - v9.26 - you will need to know the options for conversion.
Silkypix is the easy road because the tiff files are demosaiced.
This is a stacked example taken with the X-Pro1 on a double arm drive - it can be done.