RPKM value interpretation

Question

[ymd56731]

Hello,

I have RNA-Seq data from a specific cell line with three biological replicates. I would like to determine whether gene X is expressed in this cell line. This is not a comparison between different cell lines, so I am not performing DEG analysis.

I normalized the read counts to RPKM, and the value for gene X is 16. However, I’m unsure whether this value is considered high or low.
I plotted the distribution of RPKM values, which, as expected, shows many genes with a value of 0 and fewer genes with higher values. Yet, I still don’t understand how to interpret the value I obtained for gene X.

I would appreciate your assistance.

Thank you!

[rfran010]

Does the gene have exon/intron structure? I feel more confident saying a gene with low counts is expressed if on the genome browser I can see exon-specific reads... Can also help determine RPKM/counts values above noise.

Answer 1

[Asaf]

You're better off with the raw read numbers. It's a relatively simple statistical question, namely what is the probability that there are X reads along the gene if this is just noise. You'll have to decide what is the nose level of course, maybe based on intergenic regions etc.