Hi Michael, I definitely agree with you. Initially, a small set of annotation dataset were included in the package for demo and quick access.
BTW, have you encountered the error: segfault from C stack overflow? 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 2/9/10 4:08 PM, "Michael Lawrence" <[email protected]> wrote: > 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]]
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