I am having a problem with rbind in annaffy. I have a very simple annaffy table that, for the sake of illustration, I have tried to duplicate by row binding to itself (this is a simplification of a more complex problem). Here is my code: affytable.temp<-subset.affytable.on.GO.func(affytable=table, GO.TERM=common.go.hyper$"GO ID"[i], GO.Desc="GO Term") bound<-rbind(affytable.temp, affytable.temp) and the output: > bound affytable.temp affytable.temp I do not have this problem with merge, which works just fine. SessionInfo (with all packages just updated): R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: rat2302cdf affy annaffy KEGG biomaRt XML RMySQL DBI rat2302 hgu95av2 GOstats multtest genefilter survival "1.5.1" "1.8.1" "1.2.0" "1.8.1" "1.4.0" "0.97-8" "0.5-5" "0.1-9" "1.10.0" "1.10.0" "1.4.0" "1.8.0" "1.8.0" "2.20" xtable RBGL annotate GO graph Ruuid Biobase cluster RWinEdt "1.3-0" "1.6.0" "1.8.0" "1.6.5" "1.8.0" "1.8.0" "1.8.0" "1.10.2" "1.7-3" Could this be a problem with R losing track of which "rbind" function to use (i.e. generic or annaffy), is annaffy broke, or am I doing something wrong? Thanks, Mark Mark W. Kimpel MD Official Business Address: Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN 46202

Kimpel, Mark William wrote: > I am having a problem with rbind in annaffy. I have a very simple > annaffy table that, for the sake of illustration, I have tried to > duplicate by row binding to itself (this is a simplification of a more > complex problem). > > Here is my code: > > > affytable.temp<-subset.affytable.on.GO.func(affytable=table, > GO.TERM=common.go.hyper$"GO ID"[i], GO.Desc="GO Term") Looks like the correct method is not being dispatched on your aafTable. I get the same result unless I force things with bound <- annaffy:::rbind.aafTable(affytable.temp, affytable.temp) I think this is a problem due to the fact that rbind.aafTable is an S3 method and an aafTable is an S4 object. Did you email Colin Smith directly? Best, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623