[BioC] Agi4x44PreProcess - Replicated Genes Error

[Samantha England]

To the Bioconductor Community

Dear All,

Thanks to your tremendous help I have successfully been able to design my own custom annotation pack (for our custom Agilent chips) and carry out every other function of the Agi4x44PreProcess package.

My custom annotation database works perfectly for the replicated probes function (CV.rep.probes), but fails when I try to run the replicated genes function (genes.rpt.agi).

Please see my session info copied in below:

> genes.rpt.agi(dd, "zfcustomAG.db", raw.data = TRUE, WRITE.html = TRUE, REPORT = TRUE)

GENE SETS: same genes interrogated by different probes 
		FILTERING BY ControlType FLAG 
		RAW DATA: PROBES AFTER ControlType FILTERING:  43754 

	INPUT DATA: RAW 
	CHIP: zfcustomAG.db 

	PROBE SETS (NON-CTRL prob rep. x 10):	 1593 
Error in lookUp(PROBE_ID, annotation.package, "SYMBOL") : 
  No keys provided



I have googled and only found one other record of this problem.  At that point the user didn't have a custom annotation database.  Since I do have a custom database (which seems to have symbol keys if I look at the qc headers for the annotation pakcage), I am wondering what the problem might be.

Any ideas/suggestions would be very gratefully received!

Many thanks in anticipation of your help.

Best Wishes

Sam England