[BioC] Annotation of Nimblegen Zebrafish Array

[Ravi Karra]

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  The probes were derived from a variety of sources, many of which are now out of date.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).

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?

Thank you in advance.

Ravi