Dear list:
    
I am performing microarray data analysis for the first time, so please forgive me if my question is inapproppriate. 
I am analyzing Affymetrix GeneChip Human Gene 1.0 ST Array and I found that "oligo package" is ideal for this type of arrays. Then, I used it and I started with the guide of V5ExonGene.pdf that I downloaded from Bioconductor. 
I read a post from the Bioconductor Mailing List Archives that said that "probeset" and "core" map to exons and genes respectively. Thus, why core expression and probeset expression showed the same values? 
I checked mappedkeys and they are different for both of them.
Moreover I would like to study at the exon level my data, for that kind of analysis is it right to use the probeset expression?

Thanks in advance.

Ire

P.S. Here is my code:

#R version 2.12.0 (2010-10-15)
#Platform: x86_64-unknown-linux-gnu (64-bit)

### Libraries
library("affy")
library("limma")
#library("hugene10stv1cdf")
library("oligo")
library("hugene10stprobeset.db")
library("hugene10sttranscriptcluster.db")
library("pd.hugene.1.0.st.v1")
library("pd.hugene.1.1.st.v1")
library("IRanges")
library("affxparser")
library("Biobase")
library("preprocessCore")
library("Biostrings")

#==================================================
### Open files and read files

archCEL<-list.celfiles("~/Documents/MICROARRAYS/MicroarraysHebeData_Analisis/rawData", full.names=TRUE)
affyHebe <- read.celfiles(archCEL)

#==================================================
### rma

genePS<-rma(affyHebe, target="probeset")

geneCore<-rma(affyHebe, target="core")

genePS
#ExpressionSet (storageMode: lockedEnvironment)
#assayData: 257430 features, 20 samples 
#  element names: exprs 
#protocolData
#  rowNames: 01_A375_1.CEL 02_A375_2.CEL ... 20_A375_CAT_4.CEL (20
#    total)
#  varLabels: exprs dates
#  varMetadata: labelDescription channel
#phenoData
#  rowNames: 01_A375_1.CEL 02_A375_2.CEL ... 20_A375_CAT_4.CEL (20
#    total)
#  varLabels: index
#  varMetadata: labelDescription channel
#featureData: none
#experimentData: use 'experimentData(object)'
#Annotation: pd.hugene.1.0.st.v1 

geneCore
#ExpressionSet (storageMode: lockedEnvironment)
#assayData: 33297 features, 20 samples 
#  element names: exprs 
#protocolData
#  rowNames: 01_A375_1.CEL 02_A375_2.CEL ... 20_A375_CAT_4.CEL (20
#    total)
#  varLabels: exprs dates
#  varMetadata: labelDescription channel
#phenoData
#  rowNames: 01_A375_1.CEL 02_A375_2.CEL ... 20_A375_CAT_4.CEL (20
#    total)
#  varLabels: index
#  varMetadata: labelDescription channel
#featureData: none
#experimentData: use 'experimentData(object)'
#Annotation: pd.hugene.1.0.st.v1 

affyHebe
#GeneFeatureSet (storageMode: lockedEnvironment)
#assayData: 1102500 features, 20 samples 
#  element names: exprs 
#protocolData
#  rowNames: 01_A375_1.CEL 02_A375_2.CEL ... 20_A375_CAT_4.CEL (20
#    total)
#  varLabels: exprs dates
#  varMetadata: labelDescription channel
#phenoData
#  rowNames: 01_A375_1.CEL 02_A375_2.CEL ... 20_A375_CAT_4.CEL (20
#    total)
#  varLabels: index
#  varMetadata: labelDescription channel
#featureData: none
#experimentData: use 'experimentData(object)'
#Annotation: pd.hugene.1.0.st.v1 

exprs(geneCore)[1:10,1:5]
        01_A375_1.CEL 02_A375_2.CEL 03_A375_3.CEL 04_A375_4.CEL
7892501      6.909749      6.704112      6.633892      5.623717
7892502      4.980227      5.060804      4.231136      5.497120
7892503      3.321211      3.455340      3.180318      3.101057
7892504      8.177332      8.396480      8.088483      7.174240
7892505      4.767836      2.304351      2.578770      2.981808
7892506      4.932023      3.743294      3.011116      4.812062
7892507      4.123462      4.653984      4.799297      5.116502
7892508      5.006965      4.052511      2.868678      4.766367
7892509     12.518170     12.537957     12.475540     12.617325
7892510      4.830203      4.941844      3.543789      3.184837
        05_A375_PCDNA3_1.CEL
7892501             5.831844
7892502             4.146510
7892503             3.149834
7892504             8.190490
7892505             2.751765
7892506             4.160108
7892507             4.888359
7892508             5.200189
7892509            12.517495
7892510             3.698457


exprs(genePS)[1:10,1:5]
        01_A375_1.CEL 02_A375_2.CEL 03_A375_3.CEL 04_A375_4.CEL
7892501      6.909749      6.704112      6.633892      5.623717
7892502      4.980227      5.060804      4.231136      5.497120
7892503      3.321211      3.455340      3.180318      3.101057
7892504      8.177332      8.396480      8.088483      7.174240
7892505      4.767836      2.304351      2.578770      2.981808
7892506      4.932023      3.743294      3.011116      4.812062
7892507      4.123462      4.653984      4.799297      5.116502
7892508      5.006965      4.052511      2.868678      4.766367
7892509     12.518170     12.537957     12.475540     12.617325
7892510      4.830203      4.941844      3.543789      3.184837
        05_A375_PCDNA3_1.CEL
7892501             5.831844
7892502             4.146510
7892503             3.149834
7892504             8.190490
7892505             2.751765
7892506             4.160108
7892507             4.888359
7892508             5.200189
7892509            12.517495
7892510             3.698457



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