Jia, I suspect that you have an old version of ChIPpeakAnno. Could you please install the most recent version and try again. Please let me know if you still encounters problem. I just tried the example and it works. Best regards, Julie myexp = RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,1 67889600,100,1000),end=c(1555199,1560599,1565199,1573799,167893599,200 ,1200),names=c("p1","p2","p3","p4","p5","p6", "p7")),strand=as.integer(1),space=c(6,6,6,6,5,4,4)) annotatedPeak= annotatePeakInBatch(myexp, AnnotationData = literature,PeakLocForDistance = "middle") sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.6.0 limma_3.6.9 [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [5] RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.12.0 BSgenome.Ecoli.NCBI.20080805_1.3.16 [9] BSgenome_1.18.2 GenomicRanges_1.2.2 [11] Biostrings_2.18.2 IRanges_1.8.8 [13] multtest_2.6.0 Biobase_2.10.0 [15] biomaRt_2.6.0 loaded via a namespace (and not attached): [1] MASS_7.3-9 RCurl_1.4-3 splines_2.12.1 survival_2.36-2 tools_2.12.1 [6] XML_3.2-0 > On 3/9/11 11:58 PM, "Jia Jin Kee" <jiajin@umich.edu> wrote: Hi Julie, I realized that the reference manual is updated today and that the annotatePeakInBatch function now has two more arguments: PeakLocForDistance and FeatureLocForDistance. However when I tried the following R code: annPeak <- annotatePeakInBatch(peakData, AnnotationData=geneData, output="nearestStart", PeakLocForDistance="middle") I got the following error message: Error in annotatePeakInBatch(peakData, AnnotationData = geneData, output = "nearestStart", : unused argument(s) (PeakLocForDistance = "middle") And when I typed ?annotatePeakInBatch in R, I could not find PeakLocForDistance and FeatureLocForDistance in the documentation. Am I missing something here? Thanks in advance Jia Jin Kee [[alternative HTML version deleted]]

Correct. Julie On 3/10/11 9:18 AM, "Jia Jin Kee" <jiajin@umich.edu> wrote: Hi Julie, To install the most recent version of chIPpeakAnno, should I update my R version first and then do source("http://www.bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") > sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 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 GO.db_2.4.1 [5] RSQLite_0.9-3 DBI_0.2-5 AnnotationDbi_1.10.2 BSgenome.Ecoli.NCBI.20080805_1.3.16 [9] BSgenome_1.16.5 GenomicRanges_1.0.9 Biostrings_2.16.9 IRanges_1.6.17 [13] multtest_2.6.0 Biobase_2.8.0 biomaRt_2.4.0 loaded via a namespace (and not attached): [1] MASS_7.3-6 RCurl_1.4-2 splines_2.11.1 survival_2.35-8 tools_2.11.1 XML_3.2-0 On Thu, Mar 10, 2011 at 8:59 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: Jia, I suspect that you have an old version of ChIPpeakAnno. Could you please install the most recent version and try again. Please let me know if you still encounters problem. I just tried the example and it works. Best regards, Julie myexp = RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,1 67889600,100,1000),end=c(1555199,1560599,1565199,1573799,167893599,200 ,1200),names=c("p1","p2","p3","p4","p5","p6", "p7")),strand=as.integer(1),space=c(6,6,6,6,5,4,4)) annotatedPeak= annotatePeakInBatch(myexp, AnnotationData = literature,PeakLocForDistance = "middle") sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.6.0 limma_3.6.9 [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [5] RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.12.0 BSgenome.Ecoli.NCBI.20080805_1.3.16 [9] BSgenome_1.18.2 GenomicRanges_1.2.2 [11] Biostrings_2.18.2 IRanges_1.8.8 [13] multtest_2.6.0 Biobase_2.10.0 [15] biomaRt_2.6.0 loaded via a namespace (and not attached): [1] MASS_7.3-9 RCurl_1.4-3 splines_2.12.1 survival_2.36-2 tools_2.12.1 [6] XML_3.2-0 > On 3/9/11 11:58 PM, "Jia Jin Kee" <jiajin@umich.edu <http:="" jiajin@umich.edu=""> > wrote: Hi Julie, I realized that the reference manual is updated today and that the annotatePeakInBatch function now has two more arguments: PeakLocForDistance and FeatureLocForDistance. However when I tried the following R code: annPeak <- annotatePeakInBatch(peakData, AnnotationData=geneData, output="nearestStart", PeakLocForDistance="middle") I got the following error message: Error in annotatePeakInBatch(peakData, AnnotationData = geneData, output = "nearestStart", : unused argument(s) (PeakLocForDistance = "middle") And when I typed ?annotatePeakInBatch in R, I could not find PeakLocForDistance and FeatureLocForDistance in the documentation. Am I missing something here? Thanks in advance Jia Jin Kee [[alternative HTML version deleted]]