[BioC] crlmm - Infinium iSelect HD Custom Genotyping

[Matthew Ritchie]

Dear Richard,

Thanks for your email.

> We have obtained data for an custom an Infinium custum iSelect HD
> BeadChip.
> I have been able to read the data using the readIdat function, however,
> I cannot do SNP genotyping calls.
> Correct me if I'm wrong, but I have the impression that this is because
> of the lack of an existing package describing the layout of the array.
> My (very related) questions are:
> 1) Is it possible to generate an beadarray description file compatible
> with crlmm for my custom array?
> 2) Is it possible to invoke crlmm with an custom array design instead of
> the suggested Human beadarray files.

Currently we only support the main Human array types offered by Illumina
(chip specific packages are available for these from Bioconductor).  The
main issue is the requirement of our method to use training data -
Illumina provide such data for the Human arrays we support, but for custom
chip types this isn't available, which means we can't proceed as usual. 
We're hoping to address this shortcoming in upcoming releases.

Best wishes,

Matt


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