Can we directly correlate FPKM/TPM to expression?

Question

[Arindam Ghosh]

Can we directly correlate FPKM/TPM to expression? In other words, does high FPKM/TPM values mean high expression for a gene?

Or how do I find the highly expressed genes within a RNAseq sample?

Answer 1

[noorpratap.singh]

FPKM/TPM are way of normalising the read counts. Link below explaining these: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/

Now coming to other part, high FPKM/TPM values means high expression of a gene. But again this is relative to phenotype of interest and samples. If you have tumor and normal samples, an average FPKM higher value in tumors for certain genes means higher in tumors compared to normal would imply highly expressed genes in tumor.