Dear Benxia, MyPeakList is an example peak dataset. For your own analysis, you will need to read in your own peak-calling file using R data import function, e.g., yourPeak= BED2RangedData(read.table(“yourPeakfile”, sep=”\t”, header=TRUE). Then call AnnoatedPeak = annotatePeakInBatch(yourPeak, AnnotationData=TSS.human.NCBI36) assuming your data is from human. Here is a previous post addressing your question. http://grokbase.com/t/r/bioconductor/133gezh9ap/bioc-chippeakanno For specific parameter setting, please type help(annotatePeakInBatch) in a R session. For detailed information, please read the paper at http://www.biomedcentral.com/1471-2105/11/237, and the user manual at http://www.bioconductor.org/packages/2.12/bioc/vignettes/ChIPpeakAnno/ inst/doc/ChIPpeakAnno.pdf. Here is the chapter on analyzing ChIP-seq data in case you have access to the following book. Tiling Arrays Methods in Molecular Biology Volume 1067, 2013, pp 105-124 Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset If you want to read more, here are the presentations on previous Bioconductor meeting. FYI, the last one has FAQ section. http://www.bioconductor.org/help/course-materials/2012/BiocEurope2012 /ChIPpeakAnno-Zhu.pdf http://www.bioconductor.org/help/course- materials/2011/BioC2011/LabStuff/Bioc2011_ChIPpeakAnno.R http://www.bioconductor.org/help/course- materials/2011/BioC2011/LabStuff/ChIPpeakAnno-BioC2011.pdf BTW, could you please copy bioconductor@r-project.org in the subsequent emails so that others can contribute/benefit? Thanks! Best regards, Julie On 9/13/13 9:56 AM, "hubenxia123" <hubenxia123@163.com> wrote: Dear professor, My name is Benxia Hu,I am a graduate student of AnHui Univesity . I want to ask you some questions about the The ChIPpeakAnno. :> library(ChIPpeakAnno) > data(myPeakList) > data(TSS.human.NCBI36) > annotatedPeak = annotatePeakInBatch(myPeakList[1:6,], AnnotationData=TSS.human.NCBI36) > as.data.frame(annotatedPeak) I don`t know what is the myPeakList .I have analysed the ChIP- seq data.so What I have is the peak-calling files。I don`t have to do the data(myPeakList).And my reference genome is UCSC hg19,not the TSS.human.NCBI36. Thank you for your time. Benxia Hu. [[alternative HTML version deleted]]