[BioC] oligo package

[Bruno [guest]]

ok sorry ill copy and past all the steps i've done after loading the "oligo" package. 
Thanks a lot

celfiles<-list.celfiles()
> celfiles
 [1] "Titan_0026_838M_Freeman_838M_A1_A05.CEL"  "Titan_0026_838M_Freeman_838M_A1_E09.CEL"  "Titan_0026_838M_Freeman_838M_A10_B07.CEL"
 [4] "Titan_0026_838M_Freeman_838M_A2_B05.CEL"  "Titan_0026_838M_Freeman_838M_A3_C05.CEL"  "Titan_0026_838M_Freeman_838M_A3_F09.CEL" 
 [7] "Titan_0026_838M_Freeman_838M_A4_D05.CEL"  "Titan_0026_838M_Freeman_838M_A5_E05.CEL"  "Titan_0026_838M_Freeman_838M_A6_F05.CEL" 
[10] "Titan_0026_838M_Freeman_838M_A7_G05.CEL"  "Titan_0026_838M_Freeman_838M_A8_H05.CEL"  "Titan_0026_838M_Freeman_838M_A9_A07.CEL" 
[13] "Titan_0026_838M_Freeman_838M_B1_C07.CEL"  "Titan_0026_838M_Freeman_838M_B1_G09.CEL"  "Titan_0026_838M_Freeman_838M_B10_D09.CEL"
[16] "Titan_0026_838M_Freeman_838M_B2_D07.CEL"  "Titan_0026_838M_Freeman_838M_B3_E07.CEL"  "Titan_0026_838M_Freeman_838M_B4_F07.CEL" 
[19] "Titan_0026_838M_Freeman_838M_B4_H09.CEL"  "Titan_0026_838M_Freeman_838M_B5_G07.CEL"  "Titan_0026_838M_Freeman_838M_B6_H07.CEL" 
[22] "Titan_0026_838M_Freeman_838M_B7_A09.CEL"  "Titan_0026_838M_Freeman_838M_B8_B09.CEL"  "Titan_0026_838M_Freeman_838M_B9_C09.CEL" 
> pd<-read.table("phenodata.txt")
> pd<-as(pd, "AnnotatedDataFrame")
>TFdata<-read.celfiles(celfiles, phenoData=pd)
Platform design info loaded.
Reading in : Titan_0026_838M_Freeman_838M_A1_A05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A1_E09.CEL
Reading in : Titan_0026_838M_Freeman_838M_A10_B07.CEL
Reading in : Titan_0026_838M_Freeman_838M_A2_B05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A3_C05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A3_F09.CEL
Reading in : Titan_0026_838M_Freeman_838M_A4_D05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A5_E05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A6_F05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A7_G05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A8_H05.CEL
Reading in : Titan_0026_838M_Freeman_838M_A9_A07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B1_C07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B1_G09.CEL
Reading in : Titan_0026_838M_Freeman_838M_B10_D09.CEL
Reading in : Titan_0026_838M_Freeman_838M_B2_D07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B3_E07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B4_F07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B4_H09.CEL
Reading in : Titan_0026_838M_Freeman_838M_B5_G07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B6_H07.CEL
Reading in : Titan_0026_838M_Freeman_838M_B7_A09.CEL
Reading in : Titan_0026_838M_Freeman_838M_B8_B09.CEL
Reading in : Titan_0026_838M_Freeman_838M_B9_C09.CEL
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

 -- output of sessionInfo(): 

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  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 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            DBI_0.2-5                 oligo_1.22.0              Biobase_2.18.0            oligoClasses_1.20.0      
[7] BiocGenerics_0.4.0        BiocInstaller_1.8.3      

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

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