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Samantha England
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40
@samantha-england-4168
Last seen 10.2 years ago
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