[BioC] need output to contain probe x, y coordinates on array - AffyTiling

[Charles Danko]

Hi, Ann,

Sorry for the late response -- I've been traveling for the holiday.

Using x,y coordinates from the array as a unique ID should be pretty easy
with a few edits to the AnalyzeTilingCelFiles function.  I have attached an
edited version, which you should be able to use in place.  Please let me
know if you have any problems.

Your earlier question regarding the custom BPMAP file is a bit harder.  I
don't think that it is likely to happen if there are probes in the array
that are not addressed by the BPMAP file, but I am not 100% sure without
looking into it further.

Is there an easy way for you to get me the BPMAP file that you have
generated?  Perhaps send me an e-mail off list and we can work something
out.

Best,
Charles

On Wed, Dec 30, 2009 at 9:50 AM, Ann Loraine <aloraine at gmail.com> wrote:

> Greetings all,
>
> I'm attempting to process some CEL files from an Affymetrix
> Arabidopsis tiling array using AffyTiling's AnalyzeTilingCelFiles
> function.
>
> How do I tell the function to output the probe x,y coordinates from the
> array?
>
> So far as I can tell, the x and y coordinates of a probe on the array
> grid are the only truly unique identifiers for a probe on any
> microarray, and I would like to use these to cross-reference with
> other data, such as the probe positions on newer genome versions or
> even different genomes from related species.
>
> The function AnalyzeTilingCel Files appears to output the probe
> intensity values - one probe per row - but it appears to create a new
> identifier for each probe instead of using the x and y coordinates
> from the array.
>
> For example, here is an example output row:
>
> "At:TIGRv5;chr1-322"    "322"   "At:TIGRv5;chr1"        "4.43950941028621"
> "2.66476527154283"      "3.52655427353936"      "2.81831265735108"
>
> The first value in the row is meant to be the identifier for the probe
> - it uses genomic coordinates to identify the probe.
>
> However, the genomic coordinates are unstable and change from release
> to release. It would be very helpful if the output could include the
> probe's x and y coordinates from the array instead of this identifier.
>
> Is there any way to do this?
>
> Your help would be much appreciated!
>
> Sincerely,
>
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics
> University of North Carolina, Charlotte
>
> I tried recreating a BPMAP file that references the most up-to-date
> version of the genome but
>



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