Thank you for your help Nianhua. Its greatly appreciated. I followed your instructions and everything went according to plan except for that the script didn't write anything to myoutput.txt (its empty). So I guess this is were the problem resides, but i have no idea what to do about it. Any suggestions? Best regards // Johan Lindberg On Mar 5, 2007, at 6:54 PM, Nianhua Li wrote: > Hi, Johan, > > Your perl configuration may have problem. The step of converting > GenBank accessions or RefSeq accessions to Entrez Gene ids is > performed by some perl scripts. The related functions are > "fileMuncher" and ".callperl" in the LL.R of AnnBuilder. Once > AnnBuilder gets the probe to Entrez Gene mapping, all other > annotations are retrieved by pure R functions. Therefore I guess your > perl may have problem. In your previous post, I observe this warning: > > perl: warning: Setting locale failed. > perl: warning: Please check that your locale settings: > LC_ALL = (unset), > LANG = "en_SE.UTF-8" > are supported and installed on your system. > > And your sessionInfo was: >> sessionInfo() > R version 2.4.1 (2006-12-18) > i386-apple-darwin8.8.1 > > locale: > C > > This may be related to the problem. I am sure there are perl experts > on the list and they can provide very useful suggestions. > > To separate the perl problem from the AnnBuilder puzzle, please try > the following on your machine: > > 1. create a empty folder, say <tmp> > 2. copy your probe-to-GenBank mapping file > ("C:/Annb/humOligoV3.0.2.txt" ?) to <tmp> and rename to myinput.txt > 3. download ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz to > <tmp>, and unzip it to gene2accession. > 4. create an empty file named myoutput.txt > 5. copy AnnBuilder/scripts/egAccParser to <tmp> and rename to > egAccParser.pl > 6. add the following lines to the beginning of egAccParser.pl: > ----------------------------------------------------- > #!/usr/bin/perl > open(BASE, "<myinput.txt") ||="" die="" "can="" not="" open="" myinput.txt";=""> open(DATA, "<gene2accession") ||="" die="" "can="" not="" open="" gene2accession";=""> open(OUT, ">myoutput.txt") || die "Can not open myoutput.txt"; > ------------------------------------------------------ > 7. from <tmp>, run: perl egAccParser.pl > > If everything works find, myoutput.txt should contain probe-to- Entrez > Gene mapping. > > hope this is helpful > > nianhua