[BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database

[Samantha England]

To the Bioconductor Community

To the "Agi4x44PreProcess" Package Author/Maintainer: Pedro Lopez-Romero



Dear All,

I wrote for your advice last week concerning a problem I was experiencing using the "genes.rpt.agi" function in "Agi4x44PreProcess".

We are using custom-designed Agilent 4x44 arrays for zebrafish.  I have designed a custom annotation database using the SQLForge package.  This works absolutely fine for all other areas of the Agi4x44PreProcess, where a database is required.  Furthermore, I have checked that symbols have been assigned by viewing the qc headers for the annotation package.

Further to the one reply that I received last week, I have used the "traceback()" function to try and see what the problem is running genes.rpt.agi.  I'm afraid, as a relative newcomer to R, that this doesn't help me decipher the original problem, but I was wondering if anybody else might have some thoughts.  I would really like to get this package working so that I can map my probes to the chromosomes.  This will enable me to see whether there is any spatial correlation between where good and bad probes are on the chromosome.

Here is the fault code, plus the traceback result:

> 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

> traceback()
3: stop("No keys provided")
2: lookUp(PROBE_ID, annotation.package, "SYMBOL")
1: genes.rpt.agi(dd, "zfcustomAG.db", raw.data = TRUE, WRITE.html = TRUE, 
       REPORT = TRUE)

Many thanks in anticipation of your help.  I would really appreciate any help/advice that you can give me.

With Very Best Wishes

Sam England
Department of Physiology, Development & Neuroscience
University of Cambridge
Anatomy Building
Downing Street
Cambridge, CB2 3DY