[BioC] different normalized results using oneChannelGUI and oligo packages

[Javier Pérez Florido]

Dear all,
I have normalized a GeneChip Human Gene ST 1.0 dataset using oligo 
package and oneChannelGUI. I've checked that the log2 normalized values 
are different (not so different, but different). When applying limma on 
them, the statistic values (p-value, M, B and statistic t) are also 
different.

I've read that oneChannelGUI uses APT tools to summarize data and, 
maybe, that is the point: they produce similar but different normalized 
values that have an effect in the final list of differentially expressed 
genes.

For oligo, I've normalized using rma method and core as a target:
OligoEset<-rma(OligoRaw,target="core")
For oneChannelGUI, I've used the option "Load gene 1.0 ST arrays from 
.CEL files."

In both cases, the limma parameters are the same.
So, I suspect the APT tools used by oneChannelGUI has influence on the 
data. Is there a way to normalize the raw data in OneChannelGUI to 
select the subgroup (core) instead of using APT tools? I think this is 
only available in Exon Arrays.

Or may be I am wrong with these conclusions.
Any tips?
Thanks,
Javier

 > sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252  
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                 
[5] LC_TIME=Spanish_Spain.1252   

attached base packages:
[1] tools     tcltk     stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
 [1] pd.hugene.1.0.st.v1_3.0.0 oligo_1.10.0            
 [3] oligoClasses_1.8.0        oneChannelGUI_1.12.0    
 [5] preprocessCore_1.8.0      GOstats_2.12.0          
 [7] RSQLite_0.7-3             DBI_0.2-4               
 [9] graph_1.24.0              Category_2.12.0         
[11] AnnotationDbi_1.8.0       tkWidgets_1.24.0        
[13] DynDoc_1.24.0             widgetTools_1.24.0      
[15] affylmGUI_1.20.0          affyio_1.14.0           
[17] affy_1.24.0               limma_3.2.1             
[19] Biobase_2.6.0           

loaded via a namespace (and not attached):
 [1] affxparser_1.18.0 annotate_1.24.0   Biostrings_2.14.0 genefilter_1.28.0
 [5] GO.db_2.3.5       GSEABase_1.8.0    IRanges_1.4.0     RBGL_1.20.0     
 [9] splines_2.10.0    survival_2.35-7   XML_2.6-0         xtable_1.5-5