Dear All, I would like to use ChIPpeakAnno to find peaks nearest to miRNA. I loaded my bed file and created a ranged data, load mmusculus_gene_ensembl dataset through mart and annotated my peaks, and it seems ok, *test.rangedData = BED2RangedData(test.bed) mart<-useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") Annotation = getAnnotation(mart, featureType="miRNA") annotatedPeak = annotatePeakInBatch(test.rangedData, AnnotationData=Annotation) as.data.frame(annotatedPeak) * <factor> <iranges> | <character> <character> <character> <numeric> <numeric> <character> MACS_peak_109 ENSMUSG00000089245 1 [54494876, 54496209] | MACS_peak_109 + ENSMUSG00000089245 54826062 54826166 upstream numeric> <numeric> <character> -331186 329853 NearestStart Now I would like to add miRNA Id as I already did when I annotated for TSS, but something goes wrong, any ideas how to solve it? *library("org.Mm.eg.db") b<- addGeneIDs(annotatedPeak,"org.Mm.eg.db",c("symbol")) Error: No entrez identifier can be mapped by input data based on the feature_id_type. Please consider to use correct feature_id_type, orgAnn or annotatedPeak * Thanks, Paolo > traceback() 2: stop("No entrez identifier can be mapped by input data based on the feature_id_type.\nPlease consider to use correct feature_id_type, orgAnn or annotatedPeak\n", call. = FALSE) 1: addGeneIDs(annotatedPeak, "org.Mm.eg.db", c("symbol")) > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C [5] LC_TIME=Italian_Italy.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] targetscan.Mm.eg.db_0.5.0 BiocInstaller_1.4.7 org.Mm.eg.db_2.7.1 ChIPpeakAnno_2.4.0 [5] limma_3.12.1 org.Hs.eg.db_2.7.1 GO.db_2.7.1 RSQLite_0.11.1 [9] DBI_0.2-5 AnnotationDbi_1.18.1 BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.24.0 [13] GenomicRanges_1.8.7 Biostrings_2.24.1 IRanges_1.14.4 multtest_2.12.0 [17] Biobase_2.16.0 biomaRt_2.12.0 BiocGenerics_0.2.0 gplots_2.11.0 [21] MASS_7.3-19 KernSmooth_2.23-8 caTools_1.13 bitops_1.0-4.1 [25] gdata_2.11.0 gtools_2.7.0 loaded via a namespace (and not attached): [1] RCurl_1.91-1.1 splines_2.15.0 stats4_2.15.0 survival_2.36-14 tools_2.15.0 XML_3.9-4.1 [[alternative HTML version deleted]]