Dear BioC community, I am using the Ringo package for analysis of ChIP-chip experiments on the Agilent platform. While the package works wonderfully, I have some doubts regarding ordering of ChIP-enriched regions (chers) that I hope someone can clarify. Specifically, I have four biological replicates and I find that, while cher finding on the smoothed reporter signals forms nice "peaks" in the found chers, biological replicate correlation of probe intensities within the cher is not considered for ordering, and therefore many show bad reproducibility when looking at individual experiments. On the other hand, most combinations of parameters miss positive control peaks that show good reproducibility among biological replicates. As I am new to Bioconductor, I wonder whether Ringo functions or other R packages can be used to evaluate biological replicate consistency in the signals within a cher. I have skimmed through the vignettes of ACME and CMART packages, but to my understanding p values are to be calculated for each sample independently. Thanks everyone in advance for your time and help, Diego Villar Diego Villar Laboratorio 2.5.2 Tel?fono 915854442 Instituto de Investigaciones Biom?dicas "Alberto Sols" CArturo Duperier, 4 28029 Madrid