[BioC] Agi4x44PreProcess - Replicated Genes Error

[Georg Otto]

Samantha England <sje28 at cam.ac.uk> writes:


> 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
>


Hard to say what is going wrong here, since I do not use the
Agi4x44PreProcess package. Running the command that results in an error
and then running traceback() often gives you an idea what is going on.

Georg