HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH
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> HC8204T <- read.maimages(c("HC8204_US09423728_252192411868_S01_CGH_1 07_Sep09_2_1.txt", "HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_3.txt"), source="agilent",columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal", + Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName")) > HC8204T$design <- c(1,-1) > RGT <- backgroundCorrect(HC8204T, method="minimum", offset=1) > MAT <- normalizeWithinArrays(RGT, method="loess") > pros <- processCGH(MA) Error in order(MA$genes$Chr, MA$genes$Position) : argument 1 is not a vector So why does this error happens? is this the right way to analyze this data??? thanks Gabriel -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] snapCGH_1.26.0 DNAcopy_1.30.0 limma_3.12.1 loaded via a namespace (and not attached): [1] aCGH_1.34.0 affy_1.34.0 affyio_1.24.0 [4] annotate_1.34.1 AnnotationDbi_1.18.1 Biobase_2.16.0 [7] BiocGenerics_0.2.0 BiocInstaller_1.4.7 cluster_1.14.2 [10] DBI_0.2-5 genefilter_1.38.0 GLAD_2.18.0 [13] grid_2.15.1 IRanges_1.14.4 lattice_0.20-6 [16] MASS_7.3-20 multtest_2.12.0 pixmap_0.4-11 [19] preprocessCore_1.18.0 RColorBrewer_1.0-5 RSQLite_0.11.1 [22] splines_2.15.1 stats4_2.15.1 strucchange_1.4-7 [25] survival_2.36-14 tilingArray_1.34.0 tools_2.15.1 [28] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 [31] zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
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Could it be that your last line is processCGH(MA) instead of processCGH(MAT) ? b On 14 August 2012 20:14, Gabriel Wajnberg [guest] <guest at="" bioconductor.org=""> wrote: > >> HC8204T <- read.maimages(c("HC8204_US09423728_252192411868_S01_CGH_ 107_Sep09_2_1.txt", "HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_3.txt"), source="agilent",columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal", > + Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName")) >> HC8204T$design <- c(1,-1) >> RGT <- backgroundCorrect(HC8204T, method="minimum", offset=1) >> MAT <- normalizeWithinArrays(RGT, method="loess") >> pros <- processCGH(MA) > Error in order(MA$genes$Chr, MA$genes$Position) : > argument 1 is not a vector > > So why does this error happens? is this the right way to analyze this data??? > > thanks > Gabriel > > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] snapCGH_1.26.0 DNAcopy_1.30.0 limma_3.12.1 > > loaded via a namespace (and not attached): > [1] aCGH_1.34.0 affy_1.34.0 affyio_1.24.0 > [4] annotate_1.34.1 AnnotationDbi_1.18.1 Biobase_2.16.0 > [7] BiocGenerics_0.2.0 BiocInstaller_1.4.7 cluster_1.14.2 > [10] DBI_0.2-5 genefilter_1.38.0 GLAD_2.18.0 > [13] grid_2.15.1 IRanges_1.14.4 lattice_0.20-6 > [16] MASS_7.3-20 multtest_2.12.0 pixmap_0.4-11 > [19] preprocessCore_1.18.0 RColorBrewer_1.0-5 RSQLite_0.11.1 > [22] splines_2.15.1 stats4_2.15.1 strucchange_1.4-7 > [25] survival_2.36-14 tilingArray_1.34.0 tools_2.15.1 > [28] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 > [31] zlibbioc_1.2.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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No no it was just typing error sorry,... especifically I tried this way MA2 <- processCGH(MAT, method.of.averaging=mean, ID="ProbeName") ------------------------------------------------------------------- --------- -------------------------------------------------------------------- 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 -----Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: ----- To: "Gabriel Wajnberg [guest]" <guest at="" bioconductor.org=""> From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> Date: 08/14/2012 06:47PM Cc: bioconductor at r-project.org, gwajnberg at inca.gov.br, snapCGH Maintainer <marioni at="" uchicago.edu=""> Subject: Re: [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH Could it be that your last line is processCGH(MA) instead of processCGH(MAT) ? b On 14 August 2012 20:14, Gabriel Wajnberg [guest] <guest at="" bioconductor.org=""> wrote: > >> HC8204T <- read.maimages(c("HC8204_US09423728_252192411868_S01_CGH_107_Sep09 _2_1.txt" , "HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_3.txt"), source="agilent",columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal", > + Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName")) >> HC8204T$design <- c(1,-1) >> RGT <- backgroundCorrect(HC8204T, method="minimum", offset=1) >> MAT <- normalizeWithinArrays(RGT, method="loess") >> pros <- processCGH(MA) > Error in order(MA$genes$Chr, MA$genes$Position) : > argument 1 is not a vector > > So why does this error happens? is this the right way to analyze this data??? > > thanks > Gabriel > > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] snapCGH_1.26.0 DNAcopy_1.30.0 limma_3.12.1 > > loaded via a namespace (and not attached): > [1] aCGH_1.34.0 affy_1.34.0 affyio_1.24.0 > [4] annotate_1.34.1 AnnotationDbi_1.18.1 Biobase_2.16.0 > [7] BiocGenerics_0.2.0 BiocInstaller_1.4.7 cluster_1.14.2 > [10] DBI_0.2-5 genefilter_1.38.0 GLAD_2.18.0 > [13] grid_2.15.1 IRanges_1.14.4 lattice_0.20-6 > [16] MASS_7.3-20 multtest_2.12.0 pixmap_0.4-11 > [19] preprocessCore_1.18.0 RColorBrewer_1.0-5 RSQLite_0.11.1 > [22] splines_2.15.1 stats4_2.15.1 strucchange_1.4-7 > [25] survival_2.36-14 tilingArray_1.34.0 tools_2.15.1 > [28] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 > [31] zlibbioc_1.2.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > [1]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [2]http://news.gmane.org/gmane.science.biology.informatics.conductor References 1. https://stat.ethz.ch/mailman/listinfo/bioconductor 2. http://news.gmane.org/gmane.science.biology.informatics.conductor
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Unfortunately, your example isn't reproducible. However, the error message seems to suggest that MA$genes$Chr isn't a vector... More specifically, check str(MA$genes) and verify what/if you get the fields Chr and Position. b On 15 August 2012 17:17, Gabriel Wajnberg <gwajnberg at="" inca.gov.br=""> wrote: > No no it was just typing error sorry,... > > especifically I tried this way > > MA2 <- processCGH(MAT, method.of.averaging=mean, ID="ProbeName") > > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- ------ > 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 > > -----Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: ----- > > To: "Gabriel Wajnberg [guest]" <guest at="" bioconductor.org=""> > From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> > Date: 08/14/2012 06:47PM > > Cc: bioconductor at r-project.org, gwajnberg at inca.gov.br, snapCGH Maintainer > <marioni at="" uchicago.edu=""> > Subject: Re: [BioC] HELP| Agilent Sureprint data , CGH analysis with limma > and snapCGH > > Could it be that your last line is > > processCGH(MA) > > instead of > > processCGH(MAT) > > ? > > b > > On 14 August 2012 20:14, Gabriel Wajnberg [guest] > <guest at="" bioconductor.org=""> wrote: >> >>> HC8204T <- >>> read.maimages(c("HC8204_US09423728_252192411868_S01_CGH_107_Sep09_ 2_1.txt", >>> "HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_3.txt"), >>> source="agilent",columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", >>> R = "rMedianSignal", >> + Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", >> "ControlType","ProbeName")) >>> HC8204T$design <- c(1,-1) >>> RGT <- backgroundCorrect(HC8204T, method="minimum", offset=1) >>> MAT <- normalizeWithinArrays(RGT, method="loess") >>> pros <- processCGH(MA) >> Error in order(MA$genes$Chr, MA$genes$Position) : >> argument 1 is not a vector >> >> So why does this error happens? is this the right way to analyze this >> data??? >> >> thanks >> Gabriel >> >> >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] snapCGH_1.26.0 DNAcopy_1.30.0 limma_3.12.1 >> >> loaded via a namespace (and not attached): >> [1] aCGH_1.34.0 affy_1.34.0 affyio_1.24.0 >> [4] annotate_1.34.1 AnnotationDbi_1.18.1 Biobase_2.16.0 >> [7] BiocGenerics_0.2.0 BiocInstaller_1.4.7 cluster_1.14.2 >> [10] DBI_0.2-5 genefilter_1.38.0 GLAD_2.18.0 >> [13] grid_2.15.1 IRanges_1.14.4 lattice_0.20-6 >> [16] MASS_7.3-20 multtest_2.12.0 pixmap_0.4-11 >> [19] preprocessCore_1.18.0 RColorBrewer_1.0-5 RSQLite_0.11.1 >> [22] splines_2.15.1 stats4_2.15.1 strucchange_1.4-7 >> [25] survival_2.36-14 tilingArray_1.34.0 tools_2.15.1 >> [28] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 >> [31] zlibbioc_1.2.0 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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Well I think I understand.... > head(MAT$genes) Row Col FeatureNum ControlType ProbeName 1 1 1 1 1 HsCGHBrightCorner 2 1 2 2 1 DarkCorner 3 1 3 3 1 DarkCorner 4 1 4 4 0 A_14_P128532 5 1 5 5 0 A_14_P105322 6 1 6 6 0 A_14_P128090 So I need to put an MAT$genes$Chr and MAT$genes$Position , but mu probes have a lenght for example A_14_P128532 is located at Chromosome 19 , so $chr = 19 , but have a start position and end position start= 7974628 and end =7974687 , how can I put this in one vector MAT$genes$Position? Thanks ------------------------------------------------------------------- --------- -------------------------------------------------------------------- Gabriel Wajnberg Mestrando em Biologia Computacional e Sistemas - Instituto Oswaldo Cruz - Fiocruz - RJ Laborat??rio de Bioinform??tica e Biologia Computacional (LBBC) Coordena????o de Pesquisa (CPQ) Instituto Nacional de C??ncer (INCA) Rio de Janeiro - RJ Tel: (21) 3207-6546 Cel: (21) 9313-2160 -----Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: ----- To: Gabriel Wajnberg <gwajnberg at="" inca.gov.br=""> From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> Date: 08/15/2012 01:34PM Cc: "Gabriel Wajnberg [guest]" <guest at="" bioconductor.org="">, bioconductor at r-project.org, snapCGH Maintainer <marioni at="" uchicago.edu=""> Subject: Re: [BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH Unfortunately, your example isn't reproducible. However, the error message seems to suggest that MA$genes$Chr isn't a vector... More specifically, check str(MA$genes) and verify what/if you get the fields Chr and Position. b On 15 August 2012 17:17, Gabriel Wajnberg <gwajnberg at="" inca.gov.br=""> wrote: > No no it was just typing error sorry,... > > especifically I tried this way > > MA2 <- processCGH(MAT, method.of.averaging=mean, ID="ProbeName") > > > > ----------------------------------------------------------------- --------- ---------------------------------------------------------------------- > 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 > > -----Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: ----- > > To: "Gabriel Wajnberg [guest]" <guest at="" bioconductor.org=""> > From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> > Date: 08/14/2012 06:47PM > > Cc: bioconductor at r-project.org, gwajnberg at inca.gov.br, snapCGH Maintainer > <marioni at="" uchicago.edu=""> > Subject: Re: [BioC] HELP| Agilent Sureprint data , CGH analysis with limma > and snapCGH > > Could it be that your last line is > > processCGH(MA) > > instead of > > processCGH(MAT) > > ? > > b > > On 14 August 2012 20:14, Gabriel Wajnberg [guest] > <guest at="" bioconductor.org=""> wrote: >> >>> HC8204T <- >>> read.maimages(c("HC8204_US09423728_252192411868_S01_CGH_107_Sep09 _2_1.txt" , >>> "HC8204_US09423728_252192411868_S01_CGH_107_Sep09_2_3.txt"), >>> source="agilent",columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", >>> R = "rMedianSignal", >> + Rb = "rBGMedianSignal"), annotation = c("Row", "Col","FeatureNum", >> "ControlType","ProbeName")) >>> HC8204T$design <- c(1,-1) >>> RGT <- backgroundCorrect(HC8204T, method="minimum", offset=1) >>> MAT <- normalizeWithinArrays(RGT, method="loess") >>> pros <- processCGH(MA) >> Error in order(MA$genes$Chr, MA$genes$Position) : >> argument 1 is not a vector >> >> So why does this error happens? is this the right way to analyze this >> data??? >> >> thanks >> Gabriel >> >> >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] snapCGH_1.26.0 DNAcopy_1.30.0 limma_3.12.1 >> >> loaded via a namespace (and not attached): >> [1] aCGH_1.34.0 affy_1.34.0 affyio_1.24.0 >> [4] annotate_1.34.1 AnnotationDbi_1.18.1 Biobase_2.16.0 >> [7] BiocGenerics_0.2.0 BiocInstaller_1.4.7 cluster_1.14.2 >> [10] DBI_0.2-5 genefilter_1.38.0 GLAD_2.18.0 >> [13] grid_2.15.1 IRanges_1.14.4 lattice_0.20-6 >> [16] MASS_7.3-20 multtest_2.12.0 pixmap_0.4-11 >> [19] preprocessCore_1.18.0 RColorBrewer_1.0-5 RSQLite_0.11.1 >> [22] splines_2.15.1 stats4_2.15.1 strucchange_1.4-7 >> [25] survival_2.36-14 tilingArray_1.34.0 tools_2.15.1 >> [28] vsn_3.24.0 XML_3.9-4 xtable_1.7-0 >> [31] zlibbioc_1.2.0 >> >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> [1]https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> [2]http://news.gmane.org/gmane.science.biology.informatics.conductor > > References 1. https://stat.ethz.ch/mailman/listinfo/bioconductor 2. http://news.gmane.org/gmane.science.biology.informatics.conductor
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