[BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Marc Carlson
mcarlson at fhcrc.org
Tue Aug 3 18:21:22 CEST 2010
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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