Dear all, I am looking at some tiling arrays (actually, not quite tiling... they have a 50bp oligo every 100bp or so) for a given chromosome. They have been hybridised with the product of ChIP using antibodies against several chromatin proteins. I am interested in some particular genes, and as I know their location I can easily find them and see what the patter is around them. But I am also interested in just finding where these proteins bind along the chromosome. Does anybody know of a procedure (or even a package) that would be useful for this purpose? I imagine that using moving averages (or medians) with a window teh same length as my average ChIP fragment would be a way to start, but then I have to come up with a way to give probes scores etc... and I feel that I'd just be reinventing the wheel. Any ideas/pointers would be very much appreciated! Thanks! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK

On Tuesday 06 February 2007 09:02, J.delasHeras at ed.ac.uk wrote: > Dear all, > > I am looking at some tiling arrays (actually, not quite tiling... they > have a 50bp oligo every 100bp or so) for a given chromosome. > > They have been hybridised with the product of ChIP using antibodies > against several chromatin proteins. > > I am interested in some particular genes, and as I know their location > I can easily find them and see what the patter is around them. > But I am also interested in just finding where these proteins bind > along the chromosome. > > Does anybody know of a procedure (or even a package) that would be > useful for this purpose? I imagine that using moving averages (or > medians) with a window teh same length as my average ChIP fragment > would be a way to start, but then I have to come up with a way to give > probes scores etc... and I feel that I'd just be reinventing the wheel. > > Any ideas/pointers would be very much appreciated! Thanks! I have a pretty simple package here: http://watson.nci.nih.gov/twiki/bin/view/Main/MeltzerLabSoftware The method is described here in brief: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&d opt=AbstractPlus&list_uids=16939795&query_hl=8&itool=pubmed_docsum There is standard documentation available in the package. Also, the website has the equivalent of a step-by-step tutorial. If you are using Nimblegen arrays and have GFF files available, there is some code to read those files directly. Sean