Here are some Frequently Asked Questions about Partek^® Flow^® software from technical support:

Why can’t I

...

find the RPKM method on the normalization menu (I see FPKM)?

 When working with paired data it should be the case that FPKM is available, and when working with single end data RPKM should be available. These metrics are essentially analogous, but based on the underlying method used for calculation (accounting for two reads mapping to 1 fragment and not counting twice for paired end data).  Here is a simple description of the differences in calculation between RPKM and FPKM: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained. 

...