AnnotationForge::makeOrgPackage GO Ids mistake

Question

[Saber_J]

Hello everyone, I'm trying to create a custom annotation for Locusta migratoria and then run an enrichment analysis with clusterProfiler. However, i met a error when run AnnotationForge::makeorgPackage(), which returns the following error:

Populating genes table:
genes table filled
Populating gene_info table:
gene_info table filled
Populating go table:
go table filled
table metadata filled
Error in makeOrgDbFromDataFrames(data, tax_id, genus, species, dbFileName,  : 
  'goTable' GO Ids must be formatted like 'GO:XXXXXXX'

My code is :

AnnotationForge::makeOrgPackage(gene_info=gene_info,
                                go=gene2go,
                                maintainer='liXY <[e-mail]>',
                                author='liXY',
                                outputDir="E:/reKEGG/LocalOrgdb/20220416",
                                tax_id=7004,
                                genus='Locusta',
                                species='migratoria',
                                goTable="go",
                                version="1.0")

and 2 files I using :

> head(gene2go)
         GID         GO EVIDENCE
1 LOCMI17615 GO:0000003      IEA
2 LOCMI17615 GO:0003674      IEA
3 LOCMI17615 GO:0003824      IEA
4 LOCMI17615 GO:0005575      IEA
5 LOCMI17615 GO:0005622      IEA
6 LOCMI17615 GO:0005623      IEA

> head(gene_info)
         GID                                                                       Gene_Name
1 LOCMI17615 Methyltransf_11,Methyltransf_12,Methyltransf_23,Methyltransf_25,Methyltransf_31
2 LOCMI17599                                                        Lig_chan,Lig_chan-Glu_bd
3 LOCMI02434 Methyltransf_11,Methyltransf_12,Methyltransf_23,Methyltransf_25,Methyltransf_31
4 LOCMI05868                                                       N-SET,RRM_1,SET,SET_assoc
5 LOCMI15917                                                                       UCR_hinge
6 LOCMI08045                                                             EZH2_WD-Binding,SET

I don't understand why this error occurs, because my GO id matches the prompt "GO: XXXXXXXX"

[Kevin Blighe]

Please re-post on Bioconductor (https://support.bioconductor.org/) - it is more appropriate to be asked there. When posting there, please also post the link to this question on Biostars. Kevi

[Saber_J]

I re-post my question on Bioconductor. Here is the link

[Kevin Blighe]

Thank you.