[BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database

[Marc Carlson]

Hi Samantha,

Just as an additional sanity check, what do you see if you look in:

library(zfcustomAG.db)
head(toTable(zfcustomAGSYMBOL))


  Marc



On 08/03/2010 12:38 AM, Samantha England wrote:
> 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
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