[BioC] MA plots for large number of arrays

[James W. MacDonald]

Hi Juliet,

On 11/2/2011 10:23 AM, Juliet Hannah wrote:
> All,
>
> I have illumina arrays (~250)  and I was looking at the options for MA
> plots in the lumi package and the beadarray package. It seems they are
> all giving pairwise plots.
>
> When I have had a large number of Affy arrays, I have had success with
> the MAplot function in affyPLM because I believe it takes the median
> of all
> arrays and then gives me one pdf comparing each array to the reference.
>
> Does anyone know of a general function similar to this that I can use
> on a matrix.

The plotMA() function in limma will do this.

Best,

Jim


>
> Thanks!
>
> Juliet
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-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] lumi_2.6.0      nleqslv_1.9.0   methylumi_2.0.0 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>   [1] affy_1.32.0           affyio_1.22.0         annotate_1.32.0
>   [4] AnnotationDbi_1.16.0  BiocInstaller_1.2.0   DBI_0.2-5
>   [7] grid_2.14.0           hdrcde_2.15           IRanges_1.12.0
> [10] KernSmooth_2.23-6     lattice_0.20-0        MASS_7.3-16
> [13] Matrix_1.0-1          mgcv_1.7-9            nlme_3.1-102
> [16] preprocessCore_1.16.0 RSQLite_0.10.0        tools_2.14.0
> [19] xtable_1.6-0          zlibbioc_1.0.0
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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