Hi, This way it works perfectly !!! many thanks again Khademul ===================================================== On Mon, Nov 30, 2009 at 3:56 PM, Julie Zhu <julie.zhu@umassmed.edu> wrote: > Hi Khademul, > > I think querying bioMart archive data failed, could you please try to get > annotation using this method before calling annotatePeakInBatch? Thanks! > Annotation = getAnnotation(mart, featureType="TSS") > annotatedPeak = annotatePeakInBatch(myPeak, AnnotationData= Annotation) > > > Best regards, > > Julie > > > > ******************************************* > Julie Zhu, Ph.D > Research Associate Professor > Program Gene Function and Expression > University of Massachusetts Medical School > 364 Plantation Street, Room 613 > Worcester, MA 01605 > 508-856-5256 > http://www.umassmed.edu/pgfe/faculty/zhu.cfm > > > > > On 11/30/09 7:13 AM, "Khademul Islam" <khademul.islam@gmail.com> wrote: > > > Hi, > > The ChIPpeakAnno is working fine with R 2.10.0 with annotation from > TSS.NCBI36..............like following: > > library(ChIPpeakAnno) > myPeak=RangedData(IRanges(start=start,end=end,names=names),space=spa ce) > data(TSS.human.NCBI36) > annotatedPeak = annotatePeakInBatch(myPeak, > AnnotationData=TSS.human.NCBI36) > result <- as.data.frame(annotatedPeak) > > > *However, if I want to get annotation from Biomart (in stead of > TSS.human.NCBI36) archive version 51, I am getting following error: > * > > > mart <- useMart(biomart="ensembl_mart_51", > dataset="hsapiens_gene_ensembl", archive=TRUE) > Checking attributes ... ok > Checking filters ... ok > > annotatedPeak = annotatePeakInBatch(myPeak, mart, featureType="TSS") ## > or, annotatedPeak = annotatePeakInBatch(myPeak, mart=mart, > featureType="TSS") > No AnnotationData as RangedData is passed in, so now querying biomart > database for AnnotationData! > *Error in annotatePeakInBatch(myPeak, mart, featureType = "TSS") : > element 1 is empty; > the part of the args list of 'class' being evaluated was: > (AnnotationData) > *> > > > > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin9.8.0 > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPpeakAnno_1.2.0 org.Hs.eg.db_2.3.6 > > [3] GO.db_2.3.5 RSQLite_0.7-3 > > [5] DBI_0.2-4 AnnotationDbi_1.8.1 > > [7] BSgenome.Ecoli.NCBI.20080805_1.3.15 BSgenome_1.14.2 > > [9] Biostrings_2.14.8 IRanges_1.4.9 > > [11] multtest_2.2.0 Biobase_2.6.0 > > [13] biomaRt_2.2.0 > > loaded via a namespace (and not attached): > [1] MASS_7.3-4 RCurl_1.2-1 XML_2.6-0 splines_2.10.0 > [5] survival_2.35-7 tools_2.10.0 > > > > > [[ I can get annotation data from biomart (similar as "getAnnotation" > function does) without any problem..... > > mart <- useMart(biomart="ensembl_mart_51", dataset="hsapiens_gene_ensembl", > archive=TRUE) > biomart_data = > getBM(attributes=c("ensembl_gene_id","chromosome_name","start_positi on","end_position","strand"), > mart=mart) > > ]] > > > *#### So, could you please tell me how to solve this problem ??? > * > Thank you > > khademul > > [[alternative HTML version deleted]]