[BioC] Genes with Low-expression

Fangxin Hong fhong at salk.edu
Thu Apr 14 21:02:06 CEST 2005

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

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