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

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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >