[BioC] lumiHumanAll.db, GOstats

[Sean Davis]

On Thu, Jun 12, 2008 at 10:57 PM, Wei Shi <shi at wehi.edu.au> wrote:
> 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.

For affy probes, this works reasonably well.  However, for longer
probes, it might be easier to map to a transcript database like RefSeq
or Ensembl genes.

Sean

> 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
>>
>>
>>
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>