Entering edit mode
11.3 years ago
zhidong.yuan
▴
20
Hi, could anyone help me to sovle this problem? I only want to do gene enrichment analysis for a non-model organism.
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
Neilfws, you are right. Thank you very much !