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

Gabriel Wajnberg GWajnberg at inca.gov.br
Wed Aug 15 19:40:43 CEST 2012


   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
   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 <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
     > 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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     >

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