[BioC] lumiHumanAll.db, GOstats

[Sean Davis]

On Tue, Jun 10, 2008 at 1:40 AM, Al Ivens <alicat at sanger.ac.uk> wrote:
> Hi,
>
> Working with the Illumina Human WG6 chips, and lumiHumanAll.db. After
> linear model fitting and clustering, I have identified a cluster of ~130
> loci that show an interesting profile.  However, as 125 of them have no
> GeneName or EntrezID, I am struggling to figure out what they might be
> biologically.
>
> >From a closer inspection of lumiHumanALl.db, I find that approx. half of
> the features have no EntrezID, so I wasn't just unlucky with the
> constituents of my cluster!
>
> Does anyone have any recommendations as to the best approach to get
> around this problem (which came to light when I tried to run GOstats,
> which requires EntrezID for mapping of terms)?

You could use one of the illuminaHuman... (rather than
lumiHumanAll.db) annotation packages which look to have a larger
number of mapped probes.

Sean