[BioC] HELP| Agilent Sureprint data , CGH analysis with limma and snapCGH

[Gabriel Wajnberg]

   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
   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
   -----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.
     >
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