To the Bioconductor Community Dear All, Thanks to your tremendous help I have successfully been able to design my own custom annotation pack (for our custom Agilent chips) and carry out every other function of the Agi4x44PreProcess package. My custom annotation database works perfectly for the replicated probes function (CV.rep.probes), but fails when I try to run the replicated genes function (genes.rpt.agi). Please see my session info copied in below: > 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 I have googled and only found one other record of this problem. At that point the user didn't have a custom annotation database. Since I do have a custom database (which seems to have symbol keys if I look at the qc headers for the annotation pakcage), I am wondering what the problem might be. Any ideas/suggestions would be very gratefully received! Many thanks in anticipation of your help. Best Wishes Sam England

Samantha England <sje28 at="" cam.ac.uk=""> writes: > My custom annotation database works perfectly for the replicated probes function (CV.rep.probes), but fails when I try to run the replicated genes function (genes.rpt.agi). > > Please see my session info copied in below: > >> 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 > Hard to say what is going wrong here, since I do not use the Agi4x44PreProcess package. Running the command that results in an error and then running traceback() often gives you an idea what is going on. Georg