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

[Benilton Carvalho]

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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>
>