I'm using Cufflinks with Cuffdiff to compare some RNA-sequencing datasets. I'm wondering what, if any, is the lower limit for comparing FPKM values?
I have some FPKMs that are <10, but the genes are called as significantly differentially expressed between samples. Can I trust this result?
There were approximately 30M total reads per sample.
Edit: also, how come I have some genes with apparently more reads mapped, and differential expression, but no significance? E.g. FPKMs: 17.86 68.89 (0 vs 1, not significant).
I have some FPKMs that are <10, but the genes are called as significantly differentially expressed between samples. Can I trust this result?
There were approximately 30M total reads per sample.
Edit: also, how come I have some genes with apparently more reads mapped, and differential expression, but no significance? E.g. FPKMs: 17.86 68.89 (0 vs 1, not significant).
Comment