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

[Gabriel Wajnberg]

   Thank you a lot wei, it worked!!!

   ----------------------------------------------------------------------------
   --------------------------------------------------------------------
   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
   -----wei wang <biowendy at gmail.com> wrote: -----

     To: Gabriel Wajnberg <GWajnberg at inca.gov.br>
     From: wei wang <biowendy at gmail.com>
     Date: 04/20/2012 05:06PM
     Cc: bioconductor at r-project.org
     Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip on chip
     array
     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
   <[1]GWajnberg at 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: [2](21) 3207-6546
     Cel: [3](21) 9313-2160

     -----"Edwin Groot" <[4]edwin.groot at biologie.uni-freiburg.de> wrote: -----
       To: "Gabriel Wajnberg" <[5]GWajnberg at inca.gov.br>
       From: "Edwin Groot" <[6]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 <[7]GWajnberg at inca.gov.br> wrote:
       >
       >    Naming the control type ??? with what??
       >
       >

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       --

       >    -----"Edwin Groot" <[8]edwin.groot at biologie.uni-freiburg.de> wrote:
       > -----
       >
       >      To: "Gabriel Wajnberg" <[9]GWajnberg at inca.gov.br>
       >      From: "Edwin Groot" <[10]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 <[11]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

         > _______________________________________________

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References

   1. mailto:GWajnberg at inca.gov.br
   2. tel:%2821%29%203207-6546
   3. tel:%2821%29%209313-2160
   4. mailto:edwin.groot at biologie.uni-freiburg.de
   5. mailto:GWajnberg at inca.gov.br
   6. mailto:edwin.groot at biologie.uni-freiburg.de
   7. mailto:GWajnberg at inca.gov.br
   8. mailto:edwin.groot at biologie.uni-freiburg.de
   9. mailto:GWajnberg at inca.gov.br
  10. mailto:edwin.groot at biologie.uni-freiburg.de
  11. mailto:GWajnberg at inca.gov.br
  12. mailto:Bioconductor at r-project.org
  13. https://stat.ethz.ch/mailman/listinfo/bioconductor
  14. http://news.gmane.org/gmane.science.biology.informatics.conductor