Illumina Sentrix Beads Arrays

Question

[Assa Yeroslaviz]

Hi everyone,

I was wondering if anyone has ever analyze the sentrix beads arrays from Illumina.

Is there an open source software/ R package to work with this kind of arrays?

Where can I find some more information about these arrays?

Thanks

Assa

[Neilfws]

"from affymetrix"? Think you mean from Illumina.

[Assa Yeroslaviz]

you're right. I have changed it

Answer 1

[Simon Cockell]

You'll want to check out the Bioconductor lumi package, which provides methods for reading Illumina array data, QC and normalisation.

I'm sure Illumina will provide you with all the technical documentation you'd need for the specific arrays you'll be working with (eg this pdf).

[Assa Yeroslaviz]

thanks Simon,

I have seen the lumi package, but I wasn't sure, if the beads arrays are the same as the sentrix arrays. After looking into the presentation they saved on the site. i figure out, they are the same :-)

Answer 2

[Chris Evelo]

We have combined different Bioconductor packages for QC, normalisation, statistics of Illumina bead arrays with a pathway analysis approach in PathVisio using RPC access to that. That pipeline now is part of arrayanalysis.org. We recently described it in this paper.