[BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database

[Georg Otto]

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

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

> 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)
>

from your traceback result and from looking at the code of genes.rpt.agi()
the following seems to be happening:

1. The function lookup() (package annotate) is called by the function
genes.rpt.agi(). Its variable PROBE_ID is copied from
ddDUP$genes$ProbeName, i.e. your input data.

2. The function lookup() gives an error because the variable PROBE_ID is
empty.

Hence, in your input data, dd$genes$probename seems to be empty. I guess
this is a vector containing the probenames.

Hope that helps.

Georg