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

Benilton Carvalho beniltoncarvalho at gmail.com
Tue Aug 14 23:47:20 CEST 2012


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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