Gabirel,  I think the problem may be that you need to specify your idColumn
since it's not found in RG$genes.  try
X <- preprocess(RG[RG$genes$ControlT==0,], idColumn="ProbeName")


On Fri, Apr 20, 2012 at 11:35 AM, Gabriel Wajnberg <GWajnberg@inca.gov.br>wrote:

>
>   stil....
>   > X <- preprocess(RG[RG$genes$ControlType==0,])
>    Error: idColumn %in% names(myRG$genes) is not TRUE
>
>
> ----------------------------------------------------------------------------
>   --------------------------------------------------------------------
>   Gabriel Wajnberg
>   Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz -
>   Fiocruz - RJ
>   Laboratório de Bioinformática e Biologia Computacional (LBBC)
>   Coordenação de Pesquisa (CPQ)
>   Instituto Nacional de Câncer (INCA)
>   Rio de Janeiro - RJ
>   Tel: (21) 3207-6546
>   Cel: (21) 9313-2160
>    -----"Edwin Groot" <edwin.groot@biologie.uni-freiburg.de> wrote: -----
>
>     To: "Gabriel Wajnberg" <GWajnberg@inca.gov.br>
>     From: "Edwin Groot" <edwin.groot@biologie.uni-freiburg.de>
>      Date: 04/20/2012 12:17PM
>      Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip on
> chip
>     array
>      On Fri, 20 Apr 2012 11:54:52 -0300
>      Gabriel Wajnberg <GWajnberg@inca.gov.br> wrote:
>     >
>     >    Naming the control type ??? with what??
>     >
>     >
>
>
> --------------------------------------------------------------------------
>     --
>      >    -----"Edwin Groot" <edwin.groot@biologie.uni-freiburg.de> wrote:
>     > -----
>     >
>     >      To: "Gabriel Wajnberg" <GWajnberg@inca.gov.br>
>     >      From: "Edwin Groot" <edwin.groot@biologie.uni-freiburg.de>
>     >      Date: 04/20/2012 11:18AM
>     >      Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip
>     > on chip
>     >      array
>     >      On Fri, 20 Apr 2012 11:01:44 -0300
>     >       Gabriel Wajnberg <GWajnberg@inca.gov.br> wrote:
>     >      >
>      >      >    I'm testing RINGO on an agilent chip on chip array with
>     > this geo
>     >      > sample:
>      >      >    when I try preprocess this what happens:
>     >      >    > X <- preprocess(RG[RG$genes$ControlT==0,])
>     >      >    Error: idColumn %in% names(myRG$genes) is not TRUE
>      Gabriel, the Error message probably means that you misspelled the name
>     of your column.
>     Instead of  RG$genes$ControlT
>     Try  RG$genes$ControlType
>     Edwin
>     --
>      >      Gabriel, try naming your column completely:
>     >      RG$genes$ControlType
>     >      Edwin
>      >      >    so what do  I do ? How can I preprocess and normalize the
>     > data?
>     >      >    thanks
>      >      >    $genes
>     >      >      Row Col ProbeUID ControlType     ProbeName
>     >        GeneName
>     >      >    1   1   1        0           1  BrightCorner
>     >    BrightCorner
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