Gene Expression Normalized values

Question

[maryak]

I have TMM normalized Htseq-count RNA seq data.Can anybody guide me does 0 value in sample mean that gene is not expressed in this sample and some higher values of same gene in some other samples mean that gene is highly expressed in these samples? Any help in this regard will be appreciated

Answer 1

[Buffo]

No, TMM values are the read-count normalized. With RNAseq data, you can calculate the relative abundance levels of the whole transcriptome by calculating the FPKM, RPKM or TPM, or if you have control samples you can also determine the fold of change of each transcript/gene against the control. I recommend you to read about it before to procced, this lecture may help you.