Using package Ringo to analyze Agilent Chip on chip array
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@gabriel-wajnberg-5240
Last seen 8.1 years ago
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 ... $source [1] "agilent" ------------------------------------------------------------------- --------- -------------------------------------------------------------------- Gabriel Wajnberg Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz - Fiocruz - RJ Laborat??rio de Bioinform??tica e Biologia Computacional (LBBC) Coordena????o de Pesquisa (CPQ) Instituto Nacional de C??ncer (INCA) Rio de Janeiro - RJ Tel: (21) 3207-6546 Cel: (21) 9313-2160 References 1. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9267
Ringo Ringo • 1.2k views
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@gabriel-wajnberg-5240
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Naming the control type ??? with what?? ------------------------------------------------------------------- --------- -------------------------------------------------------------------- Gabriel Wajnberg Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz - Fiocruz - RJ Laborat??rio de Bioinform??tica e Biologia Computacional (LBBC) Coordena????o de Pesquisa (CPQ) Instituto Nacional de C??ncer (INCA) Rio de Janeiro - RJ Tel: (21) 3207-6546 Cel: (21) 9313-2160 -----"Edwin Groot" <edwin.groot at="" biologie.uni-freiburg.de=""> wrote: ----- To: "Gabriel Wajnberg" <gwajnberg at="" inca.gov.br=""> From: "Edwin Groot" <edwin.groot at="" biologie.uni-freiburg.de=""> Date: 04/20/2012 11:18AM Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip on chip array On Fri, 20 Apr 2012 11:01:44 -0300 Gabriel Wajnberg <gwajnberg at="" inca.gov.br=""> wrote: > > I'm testing RINGO on an agilent chip on chip array with this geo > sample: > when I try preprocess this what happens: > > X <- preprocess(RG[RG$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 > $genes > Row Col ProbeUID ControlType ProbeName GeneName > 1 1 1 0 1 BrightCorner BrightCorner
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@gabriel-wajnberg-5240
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stil.... > X <- preprocess(RG[RG$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 Laborat??rio de Bioinform??tica e Biologia Computacional (LBBC) Coordena????o de Pesquisa (CPQ) Instituto Nacional de C??ncer (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?? > > ----------------------------------------------------------------- --------- -- > -----"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 > > $genes > > Row Col ProbeUID ControlType ProbeName > GeneName > > 1 1 1 0 1 BrightCorner > BrightCorner > _______________________________________________
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Gabirel, I think the problem may be that you need to specify your idColumn since it's not found in RG$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 > > > $genes > > > Row Col ProbeUID ControlType ProbeName > > GeneName > > > 1 1 1 0 1 BrightCorner > > BrightCorner > > _______________________________________________ > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Thank you a lot wei, it worked!!! ------------------------------------------------------------------- --------- -------------------------------------------------------------------- Gabriel Wajnberg Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz - Fiocruz - RJ Laborat??rio de Bioinform??tica e Biologia Computacional (LBBC) Coordena????o de Pesquisa (CPQ) Instituto Nacional de C??ncer (INCA) Rio de Janeiro - RJ Tel: (21) 3207-6546 Cel: (21) 9313-2160 -----wei wang <biowendy at="" gmail.com=""> wrote: ----- To: Gabriel Wajnberg <gwajnberg at="" inca.gov.br=""> From: wei wang <biowendy at="" gmail.com=""> Date: 04/20/2012 05:06PM Cc: bioconductor at r-project.org Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip on chip array Gabirel, I think the problem may be that you need to specify your idColumn since it's not found in RG$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$genes) is not TRUE ------------------------------------------------------------------- --------- -------------------------------------------------------------------- Gabriel Wajnberg Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz - Fiocruz - RJ Laborat????rio de Bioinform????tica e Biologia Computacional (LBBC) Coordena????????o de Pesquisa (CPQ) Instituto Nacional de C????ncer (INCA) Rio de Janeiro - RJ Tel: [2](21) 3207-6546 Cel: [3](21) 9313-2160 -----"Edwin Groot" <[4]edwin.groot at biologie.uni-freiburg.de> wrote: ----- To: "Gabriel Wajnberg" <[5]GWajnberg at inca.gov.br> From: "Edwin Groot" <[6]edwin.groot at biologie.uni- freiburg.de> Date: 04/20/2012 12:17PM Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip on chip array On Fri, 20 Apr 2012 11:54:52 -0300 Gabriel Wajnberg <[7]GWajnberg at inca.gov.br> wrote: > > Naming the control type ??? with what?? > > ------------------------------------------------------------------- ------- -- > -----"Edwin Groot" <[8]edwin.groot at biologie.uni- freiburg.de> wrote: > ----- > > To: "Gabriel Wajnberg" <[9]GWajnberg at inca.gov.br> > From: "Edwin Groot" <[10]edwin.groot at biologie.uni- freiburg.de> > Date: 04/20/2012 11:18AM > Subject: Re: [BioC] Using package Ringo to analyze Agilent Chip > on chip > array > On Fri, 20 Apr 2012 11:01:44 -0300 > Gabriel Wajnberg <[11]GWajnberg at inca.gov.br> wrote: > > > > I'm testing RINGO on an agilent chip on chip array with > this geo > > sample: > > when I try preprocess this what happens: > > > X <- preprocess(RG[RG$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 > _______________________________________________ _______________________________________________ Bioconductor mailing list [12]Bioconductor at r-project.org [13]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [14]http://news.gmane.org/gmane.science.biology.informatics.conductor 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
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