On Thu, Mar 26, 2009 at 4:04 AM, Mattias Bair <mattias.bair@gmx.at> wrote:

> 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?
>

For doing alignments, you will probably want to do this locally on your
machine.  You can download blast, blat, gmap, or any of a number of
alignment programs.  Then, you will need the probe sequences, which you
have.  Finally, you will need the transcriptome to which you want to align,
typically in fasta format.  Run the alignments using the chosen software.
Then, you will need to postprocess your results.  Finally, you may need to
make an alternative CDF for the array based on the alignments.  What I have
described is NOT a trivial task and may require a bioinformatics
collaboration.  Finally, what I have described is just to annotate the
arrays for sheep.  Determining the meaning of the data would be a second
step.

Sean



>
> -------- Original-Nachricht --------
> > Datum: Wed, 25 Mar 2009 16:52:03 -0600
> > Von: Balasubramanian Ganesan <bala.g@aggiemail.usu.edu>
> > An: Mattias Bair <mattias.bair@gmx.at>
> > CC: bioconductor@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@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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