[BioC] Control probe QC plots for Infinium 450k chips (lumi, minfi...)

Jon Manning Jonathan.Manning at ed.ac.uk
Fri Aug 23 13:05:32 CEST 2013

Hi Bioconductors,

I'm trying to find out if there are good existing ways in Bioconductor 
of plotting out the QC data from Illumina Methylation 450k chips. I want 
to plot the control probe intensities separately for green and red 
channels, label the individual probe types properly (such as 'DNP 
(High)', 'Biotin (Med)' for the staining controls), and ideally indicate 
expected (qualitative) intensities. I've actually done this myself, but 
want to know if I've missed the BioC way.

The detail:

I have 'sample methylation profile', 'control probe profile' etc files 
(not the IDAT files). The way Lumi and friends read the controlData 
(retrievable from a controlData slot in the methyLumiM object), probe 
detail seems to be lost, such that for the staining controls ('DNP 
(High)', 'Biotin (Med)') I just get identifiers like STAINING, 
STAINING.1. The results of methylumi's qcplot() function are then 
supremely un-useful. Likewise Minfi's QC plotting functions seem from 
the docs not to label individual control types (though I don't have the 
IDAT data so Minfi isn't very useful to me anyway).

I needed to finish my work, so I brewed my own method using ggplot() and 
cross-referencing the control data and annotation from the manifest 
(outside of Lumi et al), but I feel this is something others will have 
done and that I've therefore missed something. Any pointers?

Many thanks,

Jon Manning

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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