RPKM threshold

[Rufio]

I've just started working with RNA seq data and what I found is a wide range of RPKM values. The problem is that I don´t know which is the best way to set up theshold to get rid of the "background noise". In some papers this thershold is around 0.3 RPKM but is not clrearly explained and it is higly dependent on you experiment (I asume).

I will be glad if anybody could help me!

Thanks in advance

[stavi]

Hello Rufio,

i got exactly the same problems. Could you solve them until today?

Thanks in advance

[Rufio]

Dear Stavi,

I've been asking around, and my feeling is that nobody knows exactly what to do. At these point there is no an "standarized metodology" to work the data with, and in cosequence each group is treating the data as they thing is better. Yesterday I was told actually that is not correct to work with R/FPKM values.

So no I´ve no idea yet sorry.

All the best.