[BioC] GCRMA, identical normalized values from 3 replicates

[fhong@salk.edu]

Hi list,

I kind of remember that someone mentioned this before, but wouldn't find
it in the archive.

I normalized 9 arrays ( 3 replicates for each of 3 conditions) used GCRMA.
Surprisingly, I found that for  one gene (or more) that the normalized
expression values are identical for 2 conditions (total 6 arrays) as
> light.gcrma.exprs[22497,]
189.02.CEL 189.03.CEL 189.04.CEL LER.02.CEL LER.03.CEL LER.04.CEL 194.02.CEL
  3.368551   3.368551   3.368551   3.368551   3.368551   3.368551  3.763626
194.03.CEL 194.04.CEL
  3.368551   3.349966
Note the first 6 values are identical


My question is: is it possible? and how does this happen? Since the
expression is pretty low (might not express at all), does GCRMA do
something like "flooring". I checked RMA normalized data, it has identical
values for two replicates for only one condition. If I use gcrma with
fast=FALSE, I got
> light.gcrma.exprs[22497,]
  189.02   189.03   189.04   LER.02   LER.03   LER.04   194.02   194.03
2.769276 2.706325 2.658057 2.837865 2.880565 2.781661 2.186927 2.370975
  194.04
2.554258



Although this gene itself shouldn't enter next step analysis, I just want
to make sure that nothing wrong with GCRMA algorithm.

R: 2.1.0 patched
GCRMA: 1.1.3
Window XP

R code
> light.gcrma=gcrma(data.light) ##where data.light is affy batch object.
(or light.gcrma=gcrma(data.light, fast=FALSE) )
 > light.gcrma.exprs=exprs(light.gcrma)

Thanks in advance!


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
(Phone): 858-453-4100 ext 1105