[BioC] Using package Ringo to analyze Agilent Chip on chip array

[Gabriel Wajnberg]

   I'm testing RINGO on an agilent chip on chip array with this geo sample:
   [1]http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9267
   Well, i've already understood something about the data, for example there
   are two different chips, one with probes for chromosomes 1 to 10 and other
   for chromosomes 11 to X and Y.
   So I 've got this RG vector... where $R are methilated signals and $G are
   genomic  dna  control....  and we have samples using wild type cells (
   array1_wt) and double knockouts cells (array2_dko), I would like to process
   it , normalize intensities....
   when I try preprocess this what happens:
   > X <- preprocess(RG[RG$genes$ControlT==0,])
   Error: idColumn %in% names(myRG$genes) is not TRUE
   so what do  I do ? How can I preprocess and normalize the data?
   thanks
   > show(RG)
   Loading required package: limma
   An object of class "RGList"
   $G
        array1_dko array1_wt
   [1,]  291.53850 339.50000
   [2,]   78.48148  90.24138
   [3,]   89.00000  98.46154
   [4,]  387.67860 455.17240
   [5,]  718.86670 749.81480
   41915 more rows ...
   $Gb
        array1_dko array1_wt
   [1,]         54        54
   [2,]         54        54
   [3,]         54        54
   [4,]         56        54
   [5,]         54        54
   41915 more rows ...
   $R
        array1_dko array1_wt
   [1,]   426.6538  446.3846
   [2,]    82.7037  101.9655
   [3,]   102.4333  113.1538
   [4,]   554.7857  665.8276
   [5,]  1108.6670 1008.6670
   41915 more rows ...
   $Rb
        array1_dko array1_wt
   [1,]         71        70
   [2,]         70        70
   [3,]         71        70
   [4,]         70        69
   [5,]         72        69
   41915 more rows ...
   $targets
                    FileName
   array1_dko array1_dko.txt
   array1_wt   array1_wt.txt
   $genes
     Row Col ProbeUID ControlType     ProbeName        GeneName
   1   1   1        0           1  BrightCorner    BrightCorner
   2   1   2        1          -1     (-)3xSLv1 NegativeControl
   3   1   3        2           0 A_76_P0137287             OCM
   4   1   4        4           0 A_76_P0137107            DEC1
   5   1   5        6           0 A_76_P0136934            LSM6
               SystematicName Description
   1             BrightCorner
   2          NegativeControl
   3   chr7:97264626-97264686    PROMOTER
   4 chr9:114982789-114982849    PROMOTER
   5 chr4:147454740-147454800      INSIDE
   41915 more rows ...
   $source
   [1] "agilent"

   ----------------------------------------------------------------------------
   --------------------------------------------------------------------
   Gabriel Wajnberg
   Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz -
   Fiocruz - RJ
   Laboratório de Bioinformática e Biologia Computacional (LBBC)
   Coordenação de Pesquisa (CPQ)
   Instituto Nacional de Câncer (INCA)
   Rio de Janeiro - RJ
   Tel: (21) 3207-6546
   Cel: (21) 9313-2160

References

   1. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9267