Question: Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
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gravatar for Georg Otto
9.0 years ago by
Georg Otto120
Georg Otto120 wrote:
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
annotation probe • 455 views
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