[BioC] Annotation Tools package

[Alexandre Kuhn]

Hi Yingfang,
Once you have loaded your Affymetrix annotation into R (assume it is
contained in an R object named 'annot') you could for instance select all
probe sets by subsetting the data.frame so as to select the first column

> allps<-annot[,1]

I am not sure this answers your question tough. Could you please send some
lines of code to help me understand what is going wrong?

Best, Alexandre

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Yingfang Tian
Sent: jeudi 6 août 2009 19:23
To: bioconductor at stat.math.ethz.ch
Cc: Brad Ander
Subject: Re: [BioC] Annotation Tools package

Dear Dr Kuhn:

We are Yingfang Tian and Brad Ander from the University of California at
Davis.  We are working on the cross-platform analysis of 3 platforms:
llumina Human Ref-8,  Affymetrix U133 plus 2 array, and Affymetrix human
Exon array.

We are trying to use your annotationTools package in R amd are able to at
least translate across probes from U133 arrays to Illumina, similar to the
example you give in the BMC Bioinformatics paper.   We were wondering how to
import large or entire numbers of probesets into the “myPS” object?  It may
be a basic R command, but unfortunately we rely on commercial software for
the majority of our analyses and have limited experience with R (hopefully
that can change on both fronts).

>From the paper, it seems that we can generate a list of Refseq IDs from 
>the
Affy Probesets and then use this list (set it as the “myPS” object) to pull
out the Illumina Probe ID using the refseq column as the identifier column.
We can export all these with a simple write command.  Right now, we are
thinking of bridging to/from the Exon arrays with the Unigene.  I guess we
will have to see how that works

Again, we are having success when dealing with a few probesets, but there
must be a way to get ALL probesets.  Can you please help us with this?
 Possibly
with the example command syntax?  In the paper you mention mapping all the
mouse probes across platforms, so you must have had to deal with this.

We are likely wanting to try the cross species analysis in the near future
as well, so learning how to get passed the limit of entering each
probe/gene/etc manually will be a big help.

Kind regards,

Yingfang and Brad

--
Yingfang Tian, PhD
M.I.N.D. Institute
University of California at Davis
2805 50th Street,Room 2434
Sacramento, CA  95817
Tel:916-703-0384

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