Error message working with ChIPpeakAnno
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 4 months ago
United States
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]]
Annotation GO BSgenome BSgenome Annotation GO BSgenome BSgenome • 891 views
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