Here are some Frequently Asked Questions about Partek^® Flow^® software based on real support calls.

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. 

Why don't you have RPM in your normalization?

RPM (reads per million) is the same as Total Count. Please use Total Count. 

What is a canonical transcript?

For genes with multiple transcripts, one of the transcripts is picked as the canonical transcript.  Based on the UCSC definition from the table browser,

knownCanonical - identifies the canonical isoform of each cluster ID, or gene. Generally, this is the longest isoform.