[BioC] MA plots for large number of arrays

Juliet Hannah juliet.hannah at gmail.com
Wed Nov 2 15:23:02 CET 2011


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.



> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=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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