Hi Sean, 
Thanks for your reply.  I should have been more specific.  I am mapping to the Zv9 cDNA build that I have downloaded from Ensembl.
Best, 
Ravi

On Feb 1, 2011, at 12:36 PM, Sean Davis wrote:

> 
> 
> On Tue, Feb 1, 2011 at 12:19 PM, Ravi Karra <ravi.karra@gmail.com> wrote:
> Hello all,
> 
> Thank you for maintaining this very informative mailing list.  I am currently working with some gene expression data using the Nimblegen Zebrafish 12 x135K Expression platform.  Unfortunately, my analysis has been limited by annotation.  The probes were derived from a variety of sources, many of which are now out of date.
> 
> A bit reluctantly, I would like to remap the array to the latest zebrafish genome available (Zv9) at Ensembl so that I can then use biomart for subsequent annotation.  I am able to map most of the probe sequences in the .ndf file to the Zv9 using matchPDict (basically using a minimally modified version of the code at http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Mapping-of-Affy-Probes-to-Transcrip).
> 
> Mapping expression probes to the genome is perhaps not the best way to go.  You should map, instead, to the transcripts.  This is not so big a deal for 25mers (and so the vignette using affy is probably not unjustifiable).  However, if you are using Nimblegen 50-60mers, then you ought to consider mapping to the transcripts.  If a probe does not map to a transcript, you can probably just ignore it.  An alternative is to be more exhaustive and map to things like ESTs, etc. 
>  
> 
> Once I do this, I am stuck.  How can I use these results to make an annotation file with PDInfoBuilder?  How do I handle probes that do not align with Zv9?  Can I get still use rma?
> 
> 
> Some of the probes may not align due to the probes crossing intron-exon boundaries.  These are highly relevant probes--hence my note above.
> 
> I'll leave the actual annotation details for others on the list.  Sorry, I know that was the main point of your original question.
> 
> Sean
>  


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