Hi Michael, Thank you so much for the information!
Best regards, Julie On 2/9/10 4:27 PM, "Michael Lawrence" <[email protected]> wrote: > > > 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] >> <http://[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] >>> <http://[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/da>>>> t >>>> a/ >>>> <https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno/d >>>> at%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] <http://[email protected]> >>>> " <[email protected] <http://[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] <http://[email protected]> >>>>> > >>>>> > [[alternative HTML version deleted]] >>>>> > >>>>> > _______________________________________________ >>>>> > Bioc-sig-sequencing mailing list >>>>> > [email protected] >>>>> <http://[email protected]> >>>>> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>>>> > >>>>> > >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-sig-sequencing mailing list >>>> [email protected] >>>> <http://[email protected]> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >>> > > [[alternative HTML version deleted]]
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