[BioC] Genes with Low-expression

[Fangxin Hong]

Hi list;
 I am sorry if this topic is too old, since I did read lots thread in BioC
maillist. But it seems that agreement is not yet reached.

My questions are:

(1) Do we need to filter genes with low expression before applying any
formal analysis. This step is gonna introduce additional error into final
result, but will it bring more benefit?
(Personally I think we should based on a time-course experiment we have done)

(2) If so, which method is the best or better to use? Or is there any
general steps we would adopt to find a method to filter genes?  Especially
in the case with low replication for each condition.
( For the time-course experiment I mentioned above, genes with different
profile patterns from different normalization method are ignored)

Any comment is welcome!

Fangxin


--
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu