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!
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written
by
ymd56731 •
1 answer
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.
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