[BioC] Sheep samples measured with a Affymetrix bovine array

[Mattias Bair]

Hi BALA!

My first idea was to get the gene name of the over- or underexpressed probes with the bovineACCNUM map of the bovine.db package and use those names to make a query with following tool http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9940&db=oar_refm&pgm=xmbn&EXPECT=2&DESCRIPTIONS=3&ALIGNMENTS=3&OTHER_ADVANCED=-G%205%20-E%202

Another idea was to get the probe sequences with, e.g.

bovineprobe$sequence[bovineprobe$Probe.Set.Name == "Bt.9985.1.S1_at"]

from the bovineprobe package and use those sequences to make the same query as above. But since the over- and underexpressed genes are a lot it would be a little bit time consuming to make all the queries per hand. Do you have an idea how to solve this problem or do you have a better strategy to get a value how valid the results are for the sheep samples? 

Thanks.



-------- Original-Nachricht --------
> Datum: Wed, 25 Mar 2009 16:52:03 -0600
> Von: Balasubramanian Ganesan <bala.g at aggiemail.usu.edu>
> An: Mattias Bair <mattias.bair at gmx.at>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] Sheep samples measured with a Affymetrix bovine array

> HiCan you describe to me your "first idea" in simpler terms - what do you
> expect the outcome to be? I kind of get what you want to know. I may have
> done something like what you are interested but just want to know for
> certain.
> Thanks
> BALA.
> 
> On Wed, Mar 25, 2009 at 12:22 PM, Mattias Bair <mattias.bair at gmx.at>
> wrote:
> 
> > Hi all!
> >
> > I'm currently facing a for me challenging job since I'm not an expert in
> > microarray analysis and hope to get here some advice for my data
> analysis. I
> > have to evaluate the data quality of sheep samples that have been
> measured
> > on a Affymetrix bovine chip. Meaning, what are the over-/underexpressed
> > genes from the sheep and how likely are those the right ones. Therefore,
> my
> > first idea was to make a sequence match of the probe sequence or the
> gene
> > associated to the probe on the sheep genome to get the gene of the sheep
> > sticking to the probe. NCBI provides therefore the "cross-species
> megaBLAST"
> > algorithm but it would be a daunting job. Is there a simple way to
> perform
> > such an anlysis with bioconductor? Or is there a better way to get a
> result
> > for my job?
> >
> > Thanks.
> > --
> >
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