Entering edit mode
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
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