[BioC] Anotation is not an equivalence (question regarding mouse4302.db and simmilar packages) - correction

[Vojtech Kulvait]

Hello,
first of all, thank you for great effort you made to develop Bioconductor packages.

I have a question regarding annotations. I am working now with mouse4302.db database (Mouse Genome 430 2.0 Array I guess). First of all I wanted to find all the probes matching single gene. I thought if I will find all alliasses to the gene name and then matching probes, it will be OK and then I can somehow sum expression values by gene (if there is some function or package to do so, please let me know).

What I found was, that there is not only one official symbol to each gene. Threre should be two different official symbols for single gene. On the top of it, the relation which spans probes by aliases or gene names is not equivalence. I mean if there is relation for two probes "to be marked with the allias" or "to be marked by the gene" I would expect when for example when  

1439356_at  1433512_at are marked with "Fli1" allias



1439356_at 1448189_a_at are market with "3632430F08Rik" allias

I would now expect that 1433512_at is marked by  "3632430F08Rik" alias also but it is not.

More exactly, I would expect that "to be marked with a symbol or alias" will be the same for all aliases but it is not and I dont know it is a mistake in anotation process or if there is some deeper biological explanation for that.

I am attaching code sample for testing this. Please run geneInfo("Fli1") to test.

With kind regards
Vojtech Kulvait.

geneInfo