[BioC] GCRMA, identical normalized values from 3 replicates

[Zhijin (Jean) Wu]

There are two steps where it's possible probe level data are forced to be
the same: in "fast=TRUE" version of GCRMA, intensities way below the
expected background level are forced to a same lower limit. In quantile
normalization if one probe gets the same rank across arrays, even if
its absolute observed intensity is not identical on all arrays, the
normalization converts the intensities to the same number.
 At gene level, one does not usually observe many identical measurements
unless the above happens for all or many probes in a probeset. But that is
still possible especially when the gene is probably not expressed. 

best,
Jean
> 
> 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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