[BioC] Building the tomato annotation library(Affy)

[Nianhua Li]

Dear Dr. Philip de,

>  
> which is a minimal improvement compared what was obtained first. Using unigene 
(instead of gb) did not improve it (on the contrary). The only problem
I have now
is that the GO-annotation is totally missing, whereas it is available
in the Affymetrix
annotation library. Furthermore, the CHRLOC environment is missing
(among against other
environments I guess) and this causes an inconsistency: if the
information cannot be
retrieved, why not include a vector with only NAs? At least, the (now
missing) environments
are there and (in this case: my script) won't break on it. For the
moment, I solved it
by checking whether tomato is being analysed or not, but including at
least an empty vector
is a "nicer" solution (to my opinion). And that the annotation of the
tomato array is poor:
well, we expected this. Thank you anyway for helping us out!
>  
> Regards,
>  
> Philip

We use ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz as our source
for gene to GO mappings. Unfortunately, tomato is not supported yet.
I couldn't find GO annotations for tomato genes from GO website
either: http://www.geneontology.org/GO.current.annotations.shtml .
Therefore I am curious about how Affymetrix obtained the GO
annotation. Thank you also for the suggestions about missing
annotations. We will think about it.

best

nianhua