Hi Anar,
"Khan, Anar" <anar.khan at="" agresearch.co.nz=""> writes:
> We have custom Affy chips based on proprietary sequences from a
species
> which isn't well represented in public databases. We've assigned GO
> annotations ourselves using InterProScan and other methods, because
the
> level of annotations of related species in public databases is also
very
> poor.
>
> Is it possible to feed predetermined GO annotations into GOstats (or
any
> other package which performs GO analyses), or are LocusLink IDs
always
> required to initialise the GO mappings?
Right now, the functions in GOstats need an annotation data package
that _looks like_ the BioC annotation packages produced for Affy
chips.
So one option is to use AnnBuilder to generate such a package using
the annotations you have. With such a package, GOstats should Just
Work.
That said, I'm currently working on some modifications that should
make GOstats a bit more flexible in this regard.
Best,
+ seth
