Hi there,

Fairly new to this area so will try to explain as clearly as possible. I have two RNA-Seq data sets - one corresponds to a series of cancer cell lines, the other to cell lines we are using as a model of 'normal' epithelium. The expression units of one data set are in FPKM the other RPKM. I think I superficially understand the difference between these units, in that one is used in mapping transcripts in single end sequencing the other paired end sequencing. 

My question is are these units directly comparable? The analysis I wish to carry out is fairly straight forward - I have a predefined list of around 500 genes, and simply want to compare differences in expression between the non-cancer/cancer background, in terms of which of these genes they are expressing at all as well as the relative expression levels. For which transcripts are expressed I had intended to use any value over 0 (FPKM or RPKM) as denoting expression of a transcript, but am unsure if I can compare relative abundance.

I should add that I only have access to the raw data of one dataset, the other is as a results table sent by collaborators. 
As already mentioned, 2*RPKM should be equal to FPKM , **if** you are dealing with paired end reads in both cases. 


FPKM/RPKM was intended as a approximate concentration value. **Within** an experiment, you can make comparisons between transcripts. *Between* experiments you should rather use TPM for transcripts or raw counts for genes (these vales are usually normalised with the tools like DESeq2 or edgeR).

Moreover, if you use different types of software to compute your bad numbers, comparisons will become even harder. Cufflinks uses an internal length normalisation and coverage based assumptions which you have to take into consideration when comparing.

Try to get the raw data from your collaborator, or at least the alignments.

Cheers

Michael