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

[Gabriel Wajnberg]

   Naming the control type ??? with what??

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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 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$genes) is not TRUE
     Gabriel, try naming your column completely:
     RG$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