Question: Copy Number Variation Analysis
0
gravatar for Abhi
4.9 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

Hey Guys

I have raw data(idat files) from Illumina Omni5 genotyping platform. My main interest is to find the Copy Number Variation in these samples. Any open-source packages that work with this type of datasets would be helpful to know.

I have explored crlmm and DNAcopy  from Bioconductor but just got errors processing the idat files from this platform. 

thanks!

cnv illumina • 1.9k views
ADD COMMENTlink modified 4.9 years ago by Matt Shirley8.9k • written 4.9 years ago by Abhi1.5k
1
gravatar for Matt Shirley
4.9 years ago by
Matt Shirley8.9k
Cambridge, MA
Matt Shirley8.9k wrote:

Take a look at the illuminario R package: http://f1000research.com/articles/2-264/v1. It's used by crlmm, so maybe you'll have no better luck, though if you can read the intensity values from the chips then maybe you can roll your own solution to write something like PennCNV formatted input files.

ADD COMMENTlink written 4.9 years ago by Matt Shirley8.9k

Thanks .. something to get started 

ADD REPLYlink written 4.9 years ago by Abhi1.5k
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