how to analysis HumanOmni5 Exome-4v1-2 Array data ?
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4.9 years ago
jmzeng1314 ▴ 130

I've download HumanOmni5 Exome-4v1-2 Array data from ENCODE: https://www.encodeproject.org/experiments/ENCSR112SHO/

just one sample in idat format.

ENCFF267GLV Download idat idat green channel
ENCFF769TDG Download idat idat red channel

also I've download the GenomeStudio software.

and I've watched some tutorial video in youtube.

I still can't find the way to analysis it.

any help ?

illumina microarray software error • 1.3k views
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Entering edit mode
4.9 years ago
jimmy_zeng ▴ 90

Firstly I used R package "illuminaio" to process the IDAT files to change them to a human readable text format!

just like : http://www.biotrainee.com/thread-906-1-1.html

and the donwload the mainfest files from Ilumina.

but I don't know how to get the AA,BB,AB genotype calls from Mean,NBeads,SD value for green and red channel.

I find another package"crlmm", but it's so complex, there's a algorithm I can't understand: KRLMN

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-158

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