Dear Laszlo, Thanks for your feedback and sorry for the confusion! Enhancer/Silencer here means potential enhancer/silencer, a region resides between genes not in the promoter regions or immediate downstream regions. We plan to change Enhancer.Silencer to Intergenic to avoid confusion. If you are wondering why majority of your peaks resides in the intergenic region, you could set proximal.promoter.cutoff=5000L and immediate.downstream.cutoff=5000L, and make sure the version of the transcript DB is the same as the genome used for your mapping. Hope this clears things up. Best regards, Julie On 8/22/13 2:51 PM, "László Halász" <hlsz.laszlo@gmail.com> wrote: Hello Julie, I'm a first year PhD student at University of Debrecen,and I used your Bioconductor package 'ChIPpeakAnno' to annotate my ChIP-seq data. I ran the following command: assignChromosomeRegion(my_peaks_RD, TSS, proximal.promoter.cutoff=1000L, immediate.downstream.cutoff=1000L, nucleotideLevel=FALSE, precedence=NULL, TranscriptDb=hsTx) and the results: $percentage subjectHits Exons Introns fiveUTRs threeUTRs Promoters immediateDownstream Enhancer.Silencer 0.40347702 16.94010146 0.02670069 0.08900228 0.37084285 0.29667428 82.38051443 It said that 82% of my peaks are in enhancers. So I'm confused, how the script defines an enhancer. Can you explain it to me please? Looking forward to your answer, Thank you, Laszlo Halasz [[alternative HTML version deleted]]