Hi, could anyone help me to sovle the following problem? I only want to do gene enrichment analysis for a non-model organism and ppy_GOannot.txt acquired from http://www.ebi.ac.uk/QuickGO/GAnnotation.

library("GOstats")

library("GSEABase")

library("AnnotationDbi")

ppyGO<-read.table("ppy_GOannot.txt",header=F)

head(ppyGO)

 V1  V2     V3

1 GO:0001933 IEA A2BDH2 2 GO:0005507 IEA A2BDH2 3 GO:0005634 IEA A2BDH2 4 GO:0005730 IEA A2BDH2 5 GO:0005783 IEA A2BDH2 6 GO:0005794 IEA A2BDH2

goFrome <- GOFrame(ppyGO,organism = "Pongo abelii")

Error in .testGOFrame(x, organism) : invalid GO Evidence codes: 'InterPro:IPR009003' 'InterPro:IPR001254|InterPro:IPR001314|InterPro:IPR018114' 'UniProtKB-KW:KW-0645' 'UniProtKB-KW:KW-0720' 'UniProtKB-KW:KW-0378' 'InterPro:IPR024886' 'UniProtKB-KW:KW-0807' 'InterPro:IPR000276' 'UniProtKB-KW:KW-0297' 'InterPro:IPR000725' 'UniProtKB-KW:KW-1003' 'UniProtKB-SubCell:SL-0039' 'InterPro:IPR000276|InterPro:IPR000725' 'UniProtKB-KW:KW-0552' 'UniProtKB-KW:KW-0472' 'InterPro:IPR000276|InterPro:IPR000725|InterPro:IPR017452' 'UniProtKB-KW:KW-0812' 'UniProtKB-KW:KW-0716' 'InterPro:IPR004072' 'InterPro:IPR004072|InterPro:IPR017452' 'InterPro:IPR015785' 'InterPro:IPR000719|InterPro:IPR001245' 'InterPro:IPR000719' 'InterPro:IPR011009' 'UniProtKB-KW:KW-0547' 'InterPro:IPR008280|InterPro:IPR018316' 'InterPro:IPR002453' 'InterPro:IPR002453|InterPro:IPR008280|InterPro:IPR017975|InterPro:IPR018316' 'UniProtKB-KW:KW-0342' 'UniProtKB-KW:KW-0963' 'UniProtKB-KW:KW-0206' 'InterPro:IPR000217|InterPro:IPR002453|InterPro:IPR017975' 'UniProtK

sessionInfo()

R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] GO.db_2.9.0 GSEABase_1.22.0 annotate_1.38.0
[4] GOstats_2.26.0 RSQLite_0.11.4 DBI_0.2-7
[7] graph_1.38.3 Category_2.26.0 AnnotationDbi_1.22.6 [10] Biobase_2.20.1 BiocGenerics_0.6.0

loaded via a namespace (and not attached): [1] AnnotationForge_1.2.2 genefilter_1.42.0 IRanges_1.18.2
[4] RBGL_1.36.2 splines_3.0.1 stats4_3.0.1
[7] survival_2.37-4 tools_3.0.1 XML_3.98-1.1
[10] xtable_1.7-1

Thank you!

Best wish,

Zhidong Yuan
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