Hi Julie, I'm wondering if ChIPpeakAnno is really the right place to be putting annotations. If there's something missing from the annotation collection, maybe it should be added there instead?
Michael On Tue, Feb 9, 2010 at 12:03 PM, Julie Zhu <[email protected]> wrote: > Hi, > > Please download the newest revision ChIPpeakAnno_1.3.2 from svn at > http://wiki.fhcrc.org/bioc/DeveloperPage which contains the > TSS.Arabdopsis.v8 annotation data. To simply just download the dataset, go > to > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno/dat > a/<https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno/dat%0Aa/>. > It seems taking forever to query annotation for Arabidopsis from the > biomaRt. Not sure whether segfault from C stack overflow is caused by > obtaining data for Arabidopsis since quering other species does not cause > this error. > > Best regards, > > Julie > > > ******************************************* > Lihua 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 2/8/10 9:59 AM, "[email protected]" <[email protected]> > wrote: > > > > > > > Dear bioc-sig-sequencing, > > > > 1. I would like to annotate (& graphically display in context of genome > > annotation) ChIP-Seq peaks found using Arabidopsis samples. Can someone > > comment on practical way(s) to do this? > > > > 2. For example, would the following be an appropriate approach: > > > > a. Employ ChIPpeakAnno package? > > > > b. For my ChIPSeq peaks data, would format as RangedData as page 10 of > > BasicChIPSeq.pdf handout for 11/19/09 talk of M. Morgan (for Nov. 18-20 > > conference, Seattle)? > > > > 2. Can you comment on the error message below? > > > > > >> > library(ChIPpeakAnno) > > ... > >> > library("biomaRt") > >> > listMarts() > > biomart > > 1 ensembl > > 2 snp > > 3 functional_genomics > > 4 vega > > 5 msd > > 6 bacterial_mart_3 > > 7 fungal_mart_3 > > 8 metazoa_mart_3 > > 9 plant_mart_3 > > ... > > version > > 1 ENSEMBL 56 GENES (SANGER UK) > > 2 ENSEMBL 56 VARIATION (SANGER UK) > > 3 ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK) > > 4 VEGA 36 (SANGER UK) > > 5 MSD PROTOTYPE (EBI UK) > > 6 ENSEMBL BACTERIA 3 (EBI UK) > > 7 ENSEMBL FUNGAL 3 (EBI UK) > > 8 ENSEMBL METAZOA 3 (EBI UK) > > 9 ENSEMBL PLANT 3 (EBI UK) > > ... > >> > mart = useMart("plant_mart_3") > >> > listDatasets(mart) > > dataset description > > 1 sbicolor_eg_gene Sorghum bicolor genes (Sbi1) > > 2 bdistachyon_eg_gene Brachypodium distachyon genes (Brachy1.0) > > 3 alyrata_eg_gene Arabidopsis lyrata genes (Araly1) > > 4 oindica_eg_gene Oryza sativa indica group genes (2005-01-BGI) > > 5 ptrichocarpa_eg_gene Populus trichocarpa genes (2004-12-JGI) > > 6 vvinifera_eg_gene Vitis vinifera genes (2007-12-IGGP) > > 7 athaliana_eg_gene Arabidopsis thaliana genes (TAIR9) > > ... > >> > arabdset<-useMart(biomart="plant_mart_3", dataset = > "athaliana_eg_gene") > > Checking attributes ... ok > > Checking filters ... ok > >> > TSSArabAnno<-getAnnotation(arabdset, featureType="TSS") > > Error: segfault from C stack overflow > > > > > >> > sessionInfo() > > R version 2.11.0 Under development (unstable) (2010-02-06 r51106) > > x86_64-unknown-linux-gnu > > > > 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_1.3.0 org.Hs.eg.db_2.3.6 > > [3] GO.db_2.3.5 RSQLite_0.8-2 > > [5] DBI_0.2-5 AnnotationDbi_1.9.4 > > [7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.15.4 > > [9] Biostrings_2.15.20 IRanges_1.5.40 > > [11] multtest_2.3.0 Biobase_2.7.4 > > [13] biomaRt_2.3.1 > > > > loaded via a namespace (and not attached): > > [1] MASS_7.3-5 RCurl_1.3-1 splines_2.11.0 survival_2.35-8 > > [5] tools_2.11.0 XML_2.6-0 > >> > > > > > > > Thanks, > > P. Terry > > [email protected] > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
