Dear Wencai, That is a very interesting observation! Yes, the results could be different due to the version difference in annotation dataset. You will need to use the same annotation build as the one you used for mapping your reads. Best regards, Julie On 2/28/11 12:17 AM, "Wencai Ma" <wencai_ma@126.com> wrote: Dear Julie I am now learn to use your ChIPpeakAnno R package. At the beginning of using it, I met a problem that annotation results are different when using your provided AnnotationData and my generated AnnotationData. Now I pasted the code, can you do me a favor to check why they are not the same? #1, your method library(ChIPpeakAnno) data(myPeakList) data(TSS.human.NCBI36) annotatedPeak = annotatePeakInBatch(myPeakList[1:6, ], AnnotationData = TSS.human.NCBI36) as.data.frame(annotatedPeak) #My method library(ChIPpeakAnno) data(myPeakList) mart<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl") annotation.data.ensembl.human.TSS=getAnnotation(mart, featureType="TSS") annotatedPeak1 = annotatePeakInBatch(myPeakList[1:6, ], AnnotationData =annotation.data.ensembl.human.TSS) as.data.frame(annotatedPeak1) Why different annotationdata generate different results? which one is correct? Thanks so much. Best regards, Wencai Ma UT MD Anderson Cancer Center, Houston, TX 2/27/11 [[alternative HTML version deleted]]