After a few days (3? seems like longer) of trying to patch Bioconductor's annotationTools
package I'm now giving up. The various annotation files I'm trying to use have changed in formatting since annotationTools' authors wrote the code. Whoever assembles the Affy annotation files uses different annotations for different arrays (which I guess is fine and makes sense) but that makes mapping from one array to another via a common symbol sort of tricky.
Anyway, I'm now back at step 1, trying to think about mapping human expression data into the same 'space' as mouse expression data so that a tool I have developed using mouse expression can maybe say something about human genes.
My main question is this: Is there a package in Bioconductor, which isn't annotationTools
, which will map a bioconductor expression set in one organism, via the NCBI HomoloGene db, onto a bioconductor expression set in another organism?
Assuming this doesn't exist, is there a 'standard' R-bioconductor way of building a mapping of all the probes (or all the genes) from one array to another? I've seen solutions using something called BioMart, but I'm keen not to leave the comfy world of bioconductor. The package biomaRt seems a bit over the top, as I think all I need is a little interface onto the HomoloGene file.
Ideally, what I would like as an output of this code is the expression level of all the orthologous probes from one array, where the orthology is in terms of, say, human->mouse.
Apologies for the lack of correct vocabulary, I feel I should have asked this question using set-builder notation rather than my suddenly lacking bio-english. A useful answer to this question would also be "your question makes no sense for these reasons" (then fill in the reasons).
I've written up the solution to this problem using biomaRt here: http://mikedewar.wordpress.com/2010/05/14/generating-homologues-using-biomart/ -- turns out biomaRt is awesome and easy to use!
I'd like to emphasis Alexandre's comment below, and point out that annotationTools isn't buggy, it just doesn't handle the arrays I've found in front of me! I'm going to edit the post a bit so that I've removed the implication that annotationTools is buggy.