[BioC] lumiHumanAll.db, GOstats

[Wei Shi]

Hi Al:

    I would suggest mapping the sequences of your ~130 probes to the 
genome directly using "blat" in the UCSC genome browser. You should be 
able to get genes which these probes can be sequence matched to 
(perfectly or not perfectly). And also you need to check if probes are 
matched with the exon regions of the genes. The probe sequences can be 
retrieved from Illumina's manifest file.

    Hope this helps.

Cheers,
Wei

Al Ivens 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)?
>
> Many thanks in advance.
>
> Cheers,
>
> a
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