try qc.probe.plot()



On Fri, Feb 17, 2012 at 10:46 AM, Aaron Mackey <amackey@virginia.edu> wrote:

> library("methylumi")
> barcodes <- paste(5900438005,
>                  paste(paste("R0", rep(1:6, 2), sep=""),
>                        paste("C0", rep(1:2, each=6), sep=""),
>                        sep=""),
>                  sep="_")
>
> lumi450k <- methylumIDAT(barcodes,
>                         idatPath="5900438005/")
> normLumi450k <- normalizeMethyLumiSet(lumi450k)
>
> So far so good; I can extract betas, etc.  But the qcplots won't work:
>
> qcplot(normLumi450k, controlTypes(normLumi450k)[1])
>
> Error in as.table.default(x) : cannot coerce into a table
>
> Thanks for any pointers,
>
> -Aaron
>
> > sessionInfo()
> R Under development (unstable) (2011-11-06 r57590)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] minfi_1.1.2                           lattice_0.20-0
>     ggplot2_0.8.9                         proto_0.3-9.2
>
>  [5] reshape_0.8.4                         plyr_1.7.1
>     matrixStats_0.4.3                     R.methodsS3_1.2.1
>
>  [9] methylumi_2.1.13
>  IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.6.4
>  RSQLite_0.11.1
> [13] DBI_0.2-5                             AnnotationDbi_1.17.21
>      Biobase_2.15.3                        BiocGenerics_0.1.4
>
> [17] BiocInstaller_1.3.7
>
> loaded via a namespace (and not attached):
>  [1] Biostrings_2.23.6     IRanges_1.13.24       MASS_7.3-17
> RColorBrewer_1.0-5    affyio_1.23.1         annotate_1.33.2
> beanplot_1.1
>  [8] bit_1.1-8             crlmm_1.13.9          ellipse_0.3-5
> ff_2.2-5              genefilter_1.37.0     limma_3.11.11
> mclust_3.4.11
> [15] multtest_2.11.2       mvtnorm_0.9-9992      nor1mix_1.1-3
> oligoClasses_1.17.24  preprocessCore_1.17.1 siggenes_1.29.5
> splines_2.15.0
> [22] survival_2.36-12      tools_2.15.0          xtable_1.7-0
>  zlibbioc_1.1.1
>
>        [[alternative HTML version deleted]]
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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