Genotype analyzing of infinium illumina bead array

Question

[hasani.iut6]

Hi.

I am interested to analysis genotype array of Illumina: Infinium.

I search a lot for different package and software that are good for my purpose.

GenomeStudio is the software that developed by Illumina company and has been developed for windows operating system. My problem with this software is that first, I don't know why I cannot Download it and second, I am interested to do my analysis in Linux, Ubuntu.

BeadStudio is another software that is used for my purpose. I couldn't find good information about it but i think it is the older version of GenomeStudio.

I find some R packages like crlmm and argyle. I have worked with argyle, It seems good but I think its work-flow doesn't start from the first step I mean reading .idat data to R and processing them. I have not worked with crlmm y.

Know I am really confused and I will really appreciated if any one can help me to find best package for this work.

Answer 1

[Kevin Blighe]

Sure, take a look at the beadarray R package, on Bioconductor: Quality assessment and low-level analysis for Illumina BeadArray data

The authors are quite reputable (in a good way) in this field.

A tutorial (PDF) can be found here: Analysis of Bead-summary Data using beadarray (for reading IDAT files, search for the section entitled 'Reading IDAT files')

Kevin

[hasani.iut6]

Thank you a lot I will check it out