Agilent ChIP-chip data analysis

[Liy]

Dear all,

Recently, I've got several normalized Agilent (4x44k, Yeast) ChIP-chip data in .txt format. I would like to analyse it in R (peak calling, visualization, etc.), but i can't find a proper package for it.

I've started with this article:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000227

but it uses Nimblegen data for example.

Some kind of pipeline would be useful. Can someone help me, how to analyse such data?

Sincerely,
L