Dear Philip,

Thanks for the detailed message!

It seems that the GO annotation for Arabidopsis is TAIR ID centric instead of Entrez ID centric.

It would be nice if all the org.*.*.dbs have similar data structure and mapping. 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")

Hope this works for you.

Kind regards,

Julie



On 7/12/10 4:05 PM, "pterry@huskers.unl.edu" <pterry@huskers.unl.edu> wrote:

Dear Julie,

Can you comment on the error message in the following code.

...
> library(ChIPpeakAnno)
...
> load("rd_s8_ratio_gtr4.RData")
> head(rd_s8_ratio_gtr4)
RangedData with 6 rows and 0 value columns across 1 space
        space           ranges |
  <character>        <IRanges> |
1           1 [112928, 113185] |
2           1 [123395, 123399] |
...
> mart_plant5arab <- useMart(biomart="plant_mart_5",dataset="athaliana_eg_gene")
Checking attributes ... ok
Checking filters ... ok
> Ann_arab = getAnnotation(mart_plant5arab, featureType="TSS")
> annPeak = annotatePeakInBatch(rd_s8_ratio_gtr4[1:6, ], AnnotationData = Ann_arab)
...
> dim(annPeak)
[1] 6 9
...
> library(org.At.tair.db)
> enrichedArabGO = getEnrichedGO(annPeak, orgAnn = "org.At.tair.db", maxP = 0.01, multiAdj = TRUE, minGOterm = 10, multiAdjMethod = "BH")
Error in get(paste(GOgenome, "ENSEMBL2EG", sep = "")) :
  object 'org.At.tairENSEMBL2EG' not found

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] org.At.tair.db_2.4.3                ChIPpeakAnno_1.4.1
 [3] limma_3.4.4                         org.Hs.eg.db_2.4.1
 [5] GO.db_2.4.1                         RSQLite_0.9-1
 [7] DBI_0.2-5                           AnnotationDbi_1.10.1
 [9] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.5
[11] GenomicRanges_1.0.5                 Biostrings_2.16.6
[13] IRanges_1.6.8                       multtest_2.4.0
[15] Biobase_2.8.0                       biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] MASS_7.3-5      RCurl_1.4-2     splines_2.11.1  survival_2.35-8
[5] tools_2.11.1    XML_3.1-0
>


Thanks,
Philip Terry
pterry@huskers.unl.edu



	[[alternative HTML version deleted]]

