Entering edit mode
Khademul Islam
▴
30
@khademul-islam-3826
Last seen 7.7 years ago
Hi,
This way it works perfectly !!!
many thanks again
Khademul
=====================================================
On Mon, Nov 30, 2009 at 3:56 PM, Julie Zhu <julie.zhu@umassmed.edu>
wrote:
> Hi Khademul,
>
> I think querying bioMart archive data failed, could you please try
to get
> annotation using this method before calling annotatePeakInBatch?
Thanks!
> Annotation = getAnnotation(mart, featureType="TSS")
> annotatedPeak = annotatePeakInBatch(myPeak, AnnotationData=
Annotation)
>
>
> Best regards,
>
> Julie
>
>
>
> *******************************************
> 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 11/30/09 7:13 AM, "Khademul Islam" <khademul.islam@gmail.com>
wrote:
>
>
> Hi,
>
> The ChIPpeakAnno is working fine with R 2.10.0 with annotation from
> TSS.NCBI36..............like following:
>
> library(ChIPpeakAnno)
> myPeak=RangedData(IRanges(start=start,end=end,names=names),space=spa
ce)
> data(TSS.human.NCBI36)
> annotatedPeak = annotatePeakInBatch(myPeak,
> AnnotationData=TSS.human.NCBI36)
> result <- as.data.frame(annotatedPeak)
>
>
> *However, if I want to get annotation from Biomart (in stead of
> TSS.human.NCBI36) archive version 51, I am getting following error:
> *
>
> > mart <- useMart(biomart="ensembl_mart_51",
> dataset="hsapiens_gene_ensembl", archive=TRUE)
> Checking attributes ... ok
> Checking filters ... ok
> > annotatedPeak = annotatePeakInBatch(myPeak, mart,
featureType="TSS") ##
> or, annotatedPeak = annotatePeakInBatch(myPeak, mart=mart,
> featureType="TSS")
> No AnnotationData as RangedData is passed in, so now querying
biomart
> database for AnnotationData!
> *Error in annotatePeakInBatch(myPeak, mart, featureType = "TSS") :
> element 1 is empty;
> the part of the args list of 'class' being evaluated was:
> (AnnotationData)
> *>
>
>
>
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-apple-darwin9.8.0
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] ChIPpeakAnno_1.2.0 org.Hs.eg.db_2.3.6
>
> [3] GO.db_2.3.5 RSQLite_0.7-3
>
> [5] DBI_0.2-4 AnnotationDbi_1.8.1
>
> [7] BSgenome.Ecoli.NCBI.20080805_1.3.15 BSgenome_1.14.2
>
> [9] Biostrings_2.14.8 IRanges_1.4.9
>
> [11] multtest_2.2.0 Biobase_2.6.0
>
> [13] biomaRt_2.2.0
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-4 RCurl_1.2-1 XML_2.6-0 splines_2.10.0
> [5] survival_2.35-7 tools_2.10.0
>
>
>
>
> [[ I can get annotation data from biomart (similar as
"getAnnotation"
> function does) without any problem.....
>
> mart <- useMart(biomart="ensembl_mart_51",
dataset="hsapiens_gene_ensembl",
> archive=TRUE)
> biomart_data =
> getBM(attributes=c("ensembl_gene_id","chromosome_name","start_positi
on","end_position","strand"),
> mart=mart)
>
> ]]
>
>
> *#### So, could you please tell me how to solve this problem ???
> *
> Thank you
>
> khademul
>
>
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