Question

crlmm and Illumina Infinium arrays

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Christian Ruckert ▴ 170

@christian-ruckert-3294

Last seen 4.9 years ago

Germany

I am trying to get copy number estimates for Illumina 660W-Quad and CytoSNP-12 bead arrays with package crlmm. I have successfully read in the *.idat files. But when continuing the crlmmIllumina function requires the specification of a chip description file. Are these files yet available somewhere? All I have are the manifest files (*.bpm) from GenomeStudio. Regards, Christian

crlmm crlmm • 1.5k views

ADD COMMENT • link updated 15.1 years ago by Matthew Ritchie ▴ 1000 • written 15.1 years ago by Christian Ruckert ▴ 170

score 0 · Answer 1 · 2009-04-30

Hi Christian, I'm glad to hear you were able to read in the data OK. You will need a chip specific package to proceed further, and as yet I haven't made any of these available on BioC (beta versions are sitting around on my harddrive). I'll let you know as soon as they are online. Best wishes, Matt > I am trying to get copy number estimates for Illumina 660W-Quad and CytoSNP-12 bead arrays with package crlmm. > > I have successfully read in the *.idat files. But when continuing the crlmmIllumina function requires the specification of a chip description file. Are these files yet available somewhere? All I have are the manifest files (*.bpm) from GenomeStudio. > > Regards, > > Christian