On Tue, Feb 9, 2010 at 1:21 PM, Julie Zhu <[email protected]> wrote:
> 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? > > Yes, but only in the multi-threaded context. R has a stack checking mechanism that gets confused outside of the main thread. This may or may not be relevant to your issue. Michael > > 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]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
