Oleg, Thanks for the detailed information! I tried and it works. You need input nearestStart as output parameter instead of nearest_start. By default it will calculate nearestStart. I will add better error message later. data(myPeakList) data(TSS.human.NCBI36) annotatedPeak = annotatePeakInBatch(myPeakList[1:6, ], AnnotationData = TSS.human.NCBI36,output='nearestStart', PeakLocForDistance='middle', FeatureLocForDistance='TSS') ?annotatePeakInBatch will give you more information about other parameters. Please let me know if you still have problems. Best regards, Julie On 10/21/10 10:59 AM, "Oleg Mayba" <oleg.mayba@gmail.com> wrote: Hi, Julie I encountered this problem with R 2.12.0. I just tried this with R 2.11.1 and I can't replicate the exact call because the version of ChIPpeakAnno for that R version doesn't have arguments Peak LocForDistance and FeatureLocForDistance, but it still gives me same error even if I don't specify these arguments (see below). Thanks! Oleg. > library('ChIPpeakAnno') > data(myPeakList) > ensembl=useMart('ensembl', dataset='hsapiens_gene_ensembl') Checking attributes ... ok Checking filters ... ok > TSS=getAnnotation(ensembl, featureType='TSS') > annotated_peaks=annotatePeakInBatch(myPeakList, AnnotationData=TSS, output='nearest_start', PeakLocForDistance='middle', FeatureLocForDistance='TSS') Error in annotatePeakInBatch(myPeakList, AnnotationData = TSS, output = "nearest_start", : unused argument(s) (PeakLocForDistance = "middle", FeatureLocForDistance = "TSS") > annotated_peaks=annotatePeakInBatch(myPeakList, AnnotationData=TSS, output='nearest_start') Error in annotatePeakInBatch(myPeakList, AnnotationData = TSS, output = "nearest_start") : object 'r.output' not found > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.4.2 limma_3.4.5 org.Hs.eg.db_2.4.1 [4] GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 [7] AnnotationDbi_1.10.2 BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.5 [10] GenomicRanges_1.0.9 Biostrings_2.16.9 IRanges_1.6.17 [13] multtest_2.5.14 Biobase_2.8.0 biomaRt_2.4.0 loaded via a namespace (and not attached): [1] MASS_7.3-6 RCurl_1.4-4.1 splines_2.11.1 survival_2.35-8 tools_2.11.1 XML_3.2-0.1 > On Thu, Oct 21, 2010 at 5:51 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: Oleg, I will look into this. Did you encounter this problem in R 2.11? Thanks! Best regards, Julie On 10/20/10 10:46 PM, "Oleg Mayba" <oleg.mayba@gmail.com <http:="" oleg.mayba@gmail.com=""> > wrote: Hi, Julie Thanks for putting this package out there. I seem to have encountered a bug or at least an uninformative error message (please see below) and I would appreciate a clarification. Thanks! Oleg. troublesome code snippet: library('ChIPpeakAnno') data(myPeakList) ensembl=useMart('ensembl', dataset='hsapiens_gene_ensembl') TSS=getAnnotation(ensembl, featureType='TSS') annotated_peaks=annotatePeakInBatch(myPeakList, AnnotationData=TSS, output='nearest_start', PeakLocForDistance='middle', FeatureLocForDistance='TSS') This results in: Error in annotatePeakInBatch(myPeakList, AnnotationData = TSS, output = "nearest_start", : object 'r.output' not found Here's session info: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.5.5 limma_3.5.21 [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [5] RSQLite_0.9-2 DBI_0.2-5 [7] AnnotationDbi_1.11.9 BSgenome.Ecoli.NCBI.20080805_1.3.16 [9] BSgenome_1.17.7 GenomicRanges_1.1.38 [11] Biostrings_2.17.48 IRanges_1.7.39 [13] multtest_2.5.14 Biobase_2.9.2 [15] biomaRt_2.5.1 loaded via a namespace (and not attached): [1] MASS_7.3-8 RCurl_1.4-3 splines_2.12.0 survival_2.35-8 [5] tools_2.12.0 XML_3.2-0 > [[alternative HTML version deleted]]