[BioC] Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Georg Otto
gwo at well.ox.ac.uk
Tue Aug 3 15:08:46 CEST 2010
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
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