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

[Gabriel Wajnberg]

   stil....
   > X <- preprocess(RG[RG$genes$ControlType==0,])
   Error: idColumn %in% names(myRG$genes) is not TRUE

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   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 at biologie.uni-freiburg.de> wrote: -----

     To: "Gabriel Wajnberg" <GWajnberg at inca.gov.br>
     From: "Edwin Groot" <edwin.groot at 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 at inca.gov.br> wrote:
     >
     >    Naming the control type ??? with what??
     >
     >

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     >    -----"Edwin Groot" <edwin.groot at biologie.uni-freiburg.de> wrote:
     > -----
     >
     >      To: "Gabriel Wajnberg" <GWajnberg at inca.gov.br>
     >      From: "Edwin Groot" <edwin.groot at 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 at 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
     > _______________________________________________