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=space)
data(TSS.human.NCBI36)
annotatedPeak = annotatePeakInBatch(myPeak, AnnotationData=TSS.human.NCBI36)
result <- as.data.frame(annotatedPeak)


*H**owever, 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_position","end_position","strand"),
mart=mart)

]]


*#### So, could you please tell me how to solve this problem ???*

Thank you

khademul

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