> Hi Fangxin > can you send me the R script you mentioned in your > e-mail below: > "Thanks, Robert. > I made the functions myself using the handout from the > short Course(this June), it turns out to be pretty > simple. So I would provide the R script of doing this > if somebody ask for. > Good day. > Fangxin" You guys are fast! I attached the R script below. I used ATH1 array as example, you can change it to whatever system you are using. For example, I am looking for genes (on ATH1 array) that contain "replication" in GOterm. Good luck! Fangxin ####### #function used to search for GO terms ########### GOTerm2Tag=function(term) { GTL=eapply(GOTERM,function(x) { grep(term,x at Term,value=TRUE) }) Glen=sapply(GTL,length) names(GTL[Glen>0]) } ##Example (get GOID of the terms that contain replication) GO.rep=GOTerm2Tag("replication") ######## #GO for all genes on ATH1 array ######## GO.Ath1=mget(AffyID,ath1121501GO) ##GO for all genes on ATH1 GOID.Ath1=sapply(GO.Ath1, function(x) { ##GO term for all genes on ATH1 onts=sapply(x, function(z) z$GOID) }) ######### #FUNCTION: Search for genes that contain the target GOID ######### GOID2Gene=function(GOID,GOID.Ath1) { ##GOID: target GOID you are looking in gene GOID.finder=sapply(GOID.Ath1,function(x) { grep(GOID,unlist(x),value=TRUE) }) GOID.finder.len=sapply(GOID.finder,length) names(GOID.finder.len>0) } ##Example: output AffyID of genes that has GOID "GO:0016563" > GOID2Gene("GO:0016563",GOID.Ath1) ######Example#################################### #look for all genes that involve in replication #output AffyID of all genes involving in replication ########## AffyID.rep=c() for ( i in GO.rep) { AffyID.rep=c(AffyID.rep,GOID2Gene(i,GOID.Ath1)) } AffyID.rep.unique=unique(AffyID.rep) -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong at salk.edu (Phone): 858-453-4100 ext 1105