Dear All,

I am actually working on a Transcriptomic project and I woudl like to produce one of this beautiful Go term graph that are mostly obligatory for all the transcriptome publication. I already did the annotation with trinotate software, so I have a list of Go term for each of my protein and I would like to use Bioconductor package to make a Go term graph at the level 2. Nevertheless, I am blocking at the first step.....

I am trying to import my data in goProfiles package with the basicProfiles command but I got an error message: 

> welsh.MF <- basicProfile("Desktop/test.txt", onto = "ANY", level = 2, idType ="GoTermsFrame" )
Error in lapply(X = X, FUN = FUN, ...) : object 'GOList' not found
Gene identifiers are not understood by the program

I tried to change the format of the input, which is a table with 4 columns separated by tabulation, but I always got the error. Here is a part of my input table:

GeneID    Ontology    Evidence    GOList
1    CC    C2844    GO:0005858
2    CC    C2844    GO:0005930
3    CC    C2844    GO:0005874
4    MF    C2844    GO:0005524
5    MF    C2844    GO:0016887
6    MF    C2844    GO:0003777
7    BP    C2844    GO:0003341
8    BP    C2844    GO:0021670
9    BP    C2844    GO:0070986
10    BP    C2844    GO:0008152

Does someone have an idea of what is my mistake? otherwise, is it possible that someone give me a little part of his table that he is able to import with the basicProfile command and the command file associated in order that I compare with my?

Thanks a lot in advance,

Best regards,

Nicolas