Dingxia,

There is no Annotation dataset in the package you loaded.

I would recommend you read the documentation about data function by typing in R ?data and also typing ?annotatePeakInBatch  and run a few examples.

Best regards,

Julie


On 8/29/12 4:25 PM, "Dingxia Feng" <fengdxia@iastate.edu> wrote:

Hi, Julie,
I got jammed again. here is what happed:
> library (ChIPpeakAnno)
> mart=useMart("WS220",dataset="wormbase_gene")
> TSS = getBM(c("gene", "chromosome_name", "chromosome_start",
+             "chromosome_end", "chromosome_strand"), mart = mart)
> TSS = unique(TSS[!is.na <http://is.na> (TSS[,3]),])
> Annotation = RangedData(IRanges(start = as.numeric(TSS[, 3]), end = as.numeric(TSS[,
+             4]), names = as.character(TSS[, 1])), strand = TSS[,
+             5], space = as.character(TSS[,
+             2]))
> MyPeakList = BED2RangedData(read.table("TSpeakList.bed", sep= "\t",header=FALSE, skip=1))
> data(myPeakList)
> data(Annotation)
Warning message:
In data(Annotation) : data set ‘Annotation’ not found

 What shall I do to fix this? Thanks.

Best.

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