Entering edit mode
Fangxin Hong
▴
810
@fangxin-hong-912
Last seen 10.2 years ago
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