[BioC] lumiHumanAll.db, GOstats

[Lynn Amon]

´The illuminaHuman... annotation packages are based on accession IDs 
taken from BLAST results from Nuno Barbosa-Marais.  Check out 
www.compbio.group.cam.ac.uk for more details.
Lynn

Sean Davis wrote:
> 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
>
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