Dear Philip,

I believe you can use biomaRt in R to convert ensembl ID to TAIR ID.

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
ensembl = useMart("ensembl")
listDatasets(ensembl)
Once the dataset is identified, use the following example to select the dataset.
hg = useDataset("hsapiens_gene_ensembl",mart=ensembl)
The getBM function can be used to obtain both EnsemblIDs and TAIR IDs.

I Cced the Bioconductor mailing list so that the biomaRt developers can chime in. Thanks!

Kind regards,

Julie


On 7/16/10 3:50 PM, "pterry@huskers.unl.edu" <pterry@huskers.unl.edu> wrote:

Dear Julie,

Concerning your suggestion regarding "getEnrichedGO" and the Arabidopsis genome,

annPeak = annotatePeakInBatch(rd_s8_ratio_gtr4[1:6, ], AnnotationData = Ann_arab)

"... For now, I would suggest call getEnrichedGO function with a list of TAIR IDs using the following syntax. You need to first convert the list of Ensembl ID to TAIR ID first.

enrichedGO.Arab <- getEnrichedGO (tarIDs, feature_id_type="entrez_id", orgAnn=""org.At.tair.db",
maxP=0.05, multiAdj =TRUE, minGOterm=10,  multiAdjMethod="BH")
"

I assume I need to convert Ensembl IDs in "annPeak" to TAIR IDs?  I note 3 columns of these IDs in the "annPeak" RangedData object (only 2 when coerced to a dataframe).  Can you recommend a way to convert these columns?  I'm still learning Bioconductor.



Thanks,
Philip Terry
pterry@huskers.unl.edu


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