Affy Tiling Array Analysis

[Liy]

Hi all,

Can someone help me suggest, an easy way to identify peaks from affymetrix ChIP-chip .CEL files?
I tried affy package (enviroment problem), and Starr. Is there any softwere, that can process .CEL/.bar files easily and give a bed file for output?

Thank you!
Liy

[GenoMax]

Simon had pointed out ChIP-Monk in a past post for this purpose: http://www.bioinformatics.babraham.a...ects/chipmonk/ It is for nimbelgen arrays so I am not sure if it can handle Affy files.

General bioconductor resources for arrays: http://www.bioconductor.org/help/wor.../oligo-arrays/

[Dario1984]

The regionStats function from the Repitools package.