Bioconductor Package for import and analysis of Illumina HumanOmni2.5-4v1_c?

Question

[brianscomer]

Hi All:

I am fairly new to bioinformatics and just obtained a dataset generated by the Illumina HumanOmni2.5-4v1_C platform. I need to determine if there is a package that will allow me to import and annotate the raw data starting from the idat files. I have the annotation files from ilumina but have not been able to find a package that will automate the import/annotation process.

The only thing thus far I have come across is illuminaio which has readIDAT() but this only works for individual idat files.

Thanks, Brian

Answer 1

[Deepak Tanwar]

This is to do something with your programming skills.

List all the files in the directory with list.files() function and then read all files using lappy() function.

Answer 2

[andrew.j.skelton73]

I think you should take a look at the CRLMM package in bioconductor.

[brianscomer]

Thanks. I actually already tried it but was told in a warning that the package was not compatible with my platform. I think the built-in annotations do not cover this version but they covered an earlier annotation version (I don't remember which at the moment but it might have been 2.5-4v1_b) of the platform.

[andrew.j.skelton73]

The CRLMM package is the only real open source solution to Genotyping your chips. As an alternative, you can ask whoever did your arraying to give you imputed plink friendly files, or at least plink friendly files and you can do the imputation yourself. Illumina's GenomStudio is what you need to do the genotyping, but it's licensed software.