[BioC] oligo package

[Bruno [guest]]

Hi all,
I've been working on R/Bioconductor for the last month and i'm still quite confused on many ways. Im currently trying to process an expression microarray dataset with Affymetrix chip (hugene.1.1.st.v1). Questions are actually multiple. I get an error when im trying to load the phenodata with the read.celfiles command saying sample names are different between phenodata and protocol data and phenodata and featuredata:
Error in validObject(out) :
  invalid class “GeneFeatureSet” object: 1: sampleNames differ between assayData and phenoData
invalid class “GeneFeatureSet” object: 2: sampleNames differ between phenoData and protocolData
 Also i have no clues how to annotate my expression data as i cant even find commands to access the annotation package. Sorry for the non-precise questions. I tried to read as much as i could and asked everyone in the dep but im still stuck here. Thank you very much
Bruno

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] pd.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2           
[3] DBI_0.2-5                 oligo_1.22.0             
[5] Biobase_2.18.0            oligoClasses_1.20.0      
[7] BiocGenerics_0.4.0       

loaded via a namespace (and not attached):
 [1] affxparser_1.30.0     affyio_1.26.0         BiocInstaller_1.8.3  
 [4] Biostrings_2.26.2     bit_1.1-9             codetools_0.2-8      
 [7] ff_2.2-10             foreach_1.4.0         GenomicRanges_1.10.5 
[10] IRanges_1.16.4        iterators_1.0.6       parallel_2.15.1      
[13] preprocessCore_1.20.0 splines_2.15.1        stats4_2.15.1        
[16] tools_2.15.1          zlibbioc_1.4.0  

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