Error In .Testgoframe(X, Organism)

Question

[zhidong.yuan]

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

Answer 1

[Neilfws]

The error says "invalid GO evidence codes".

It looks as though column V2 in your data frame contains names, such as InterPro accessions, which are not GO evidence codes. Valid codes are terms like IEA, which you have shown.

[zhidong.yuan]

Neilfws, you are right. Thank you very much !