Hello! I have been processing some ChIP-seq data and I looked through the literature and it seemed that spp is indicated as a good program to use. I have found and adapted the two tutorials I found for using spp, https://sites.google.com/a/brown.edu/bioinformatics-in- biomed/spp-r-from-chip-seq and http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html I have also read the paper. My question is about the MSER and the predicted sequencing depth - additional output of spp. So what I think the MSER is, is the score value above which a peak is authoritatively determined? When I look at peaks above this score value they are very well defined. Also, is the predicted sequencing depth is a prediction of the number of additional "tags" necessary so that the MSER and the FDR value coincide? I know that this isn't a bioconductor package, but I think that there are probably quite a few people on this list that are using it and it is hard to find decent information about this program. Any advice or additional information is greatly appreciated! TIA Matt Matthew E. Thornton Research Lab Specialist Saban Research Institute USC/Children?s Hospital Los Angeles 513X, Mail Stop 35 4661 W. Sunset Blvd. Los Angeles, CA 90027-6020 matthew.thornton at med.usc.edu