Hi Benilton & all, I've gotten some data from Affy's mouse promoter 1.0R tiling array, and I'm trying to figure out how to analyze it. I've looked in the archives, and found some of your posts about the oligo and makePlatformDesign packages very helpful: https://stat.ethz.ch/pipermail/bioconductor/2007-January/015655.html https://stat.ethz.ch/pipermail/bioconductor/2006-August/014167.html My question: what's the meaning of the different arguments for makePDpackage? In your tutorial slides from BioC2006, you show it called along these lines: makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", genomebuild="mg33") However, in the August post above, it was being used this way: makePDpackage("Hs_PromPF_v02-3_NCBIv34.bpmap", file1="Hs_PromPF_v02.cif", manufacturer="affymetrix", type="tiling") What is the file1 argument? The help page doesn't say what these should be for tiling arrays, and it appears from your tutorial that it's not necessary. For the mouse promoter tiling array, there are two .cif files, one forward and one reverse. Here's what Affy's readme file said about them: "The R and F tiling sets have been split into two separate zip files so make sure you have the right file." Should I be using these? How should I be using these? My first goal is just to look at the raw data values, and there are only 2 arrays - one CHip and one control. The researchers want see how well these arrays turned out, and get some idea on what level of replication may be needed. And if anyone knows any good articles on analyzing CHip-on-chip arrays, please point them out to me - I've been finding some, but I would like to know what others have found useful. Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu