[BioC] GCRMA, identical normalized values from 3 replicates

[Adaikalavan Ramasamy]

RMA and GCRMA use quantile normalization step at individual probe level.
It is possible to get identical values after summarising these values. I
recently had constant value across 6 arrays for a particular gene. But I
guess any kind of oddity might happen with 50,000+ genes.

Regards, Adai



On Thu, 2005-08-11 at 11:28 -0700, fhong at salk.edu wrote:
> 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
> 
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