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" <lawrence.michael@gene.com> 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 <julie.zhu@umassmed.edu> 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, "pterry@huskers.unl.edu" <pterry@huskers.unl.edu> 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
>>> > pterry@huskers.unl.edu
>>> >
>>> >         [[alternative HTML version deleted]]
>>> >
>>> > _______________________________________________
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>>> > Bioc-sig-sequencing@r-project.org
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>> >
>>> >
>> 
>> 
>> 
>>         [[alternative HTML version deleted]]
>> 
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> 
> 


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