[BioC] Annotation in Agi4x44PreProcess

[Samantha England]

To the Maintainers of "Agi4x44PreProcess" and the Bioconductor community

We are using custom-designed Agilent chips (4 x 45220 probe) to analyse one-colour samples prepared from zebrafish embryos.  The question I have concerns the use of annotation databases in "Agi4x44PreProcess".  

The raw text files generated by the Agilent Feature Extraction software contain the probe and gene name for each spot on the array.  We also have a custom designed gal file.  The problem we have is that only 5 zebrafish-specific annotation databases exist for zebrafish: four of these have been designed for use with the Affymetrix zebrafish chip, whilst the remaining database uses entrez ids.  Our gene names are predominantly listed as ENSEMBL transcript identifiers (only a small proportion are entrez ids).  Therefore there doesn't yet exist an appropriate annotation database for use with our data.  With this in mind I have two questions:

Firstly, is it possible to run the Agi4x44PreProcess software successfully without calling an annotation database (can the probe ids within the .txt files be used to identify the replicated probes)?  Secondly, if it is not possible to run the Agi4x44PreProcess software without using an annotation database, is there any way that we could somehow use the gal file instead?

I apologise in advance if these are naive questions - I am a newbie to microarrays and all thing r and would appreciate any advice that you can give me.

Many thanks in anticipation of your help.

Best Wishes

Samantha (Sam) England
Department of Physiology, Development & Neuroscience
University of Cambridge