Dear John, sorry, I forgot to give this information: R 2.0.1 on Mac OS 10.2.8 AnnBuilder 1.4.21 Here are the first two lines of the annotation matrix. For reasons that I do not understand, the first line is empty. Could this be the reason for the error? And is there a way to circumvent this? > annotation[1:2,] PROBE ACCNUM LOCUSID UNIGENE "" "" "NA" "NA" CGENZEB_456000002_0 "CGENZEB_456000002_0" "AF030031" "30131" "Dr.30326" GENENAME SYMBOL CHR MAP PMID GRIF "NA" "NA" "NA" "NA" "NA" "NA" CGENZEB_456000002_0 "deltaA" "dla" "1" "NA" "12890499;12835391;12477932" "NA" SUMFUNC "NA" CGENZEB_456000002_0 "NA" GO "NA" CGENZEB_456000002_0 "GO:0005509@IEA;GO:0007154@IEA;GO:0009880@IMP;GO:0016020@IEA;GO:000551 5@ IDA" OMIM REFSEQ "NA" "NA" CGENZEB_456000002_0 "NA" "NM_130954;NP_571029" Best, Georg > >>> pkgName<-"test" >>> pkgPath<-getwd() >>> createEmptyDPkg(pkgName, pkgPath, force=TRUE) >>> annotation<-as.matrix(annotation) > > What did annotation contain? Did annotation have column names? You > need to > provide us with more information (e. g. R version, AnnBuilder version, > more > example code) > > >> >> then I get the following error: >> >>> writeAnnData2Pkg(annotation, pkgName, pkgPath) >> >> Error in assign(x[i], value[[i2]], envir = envir, inherits = >> inherits) : >> attempt to use zero-length variable name >> >> >> Could someone give me a hint what is wrong here? >> >> Best, >> >> Georg >> >> P.S. I am on digest mode, cc'ing the answer directly to me would be >> nice -- Georg Wilhelm Otto Max-Planck-Institute for Developmental Biology Spemannstrasse 35/III D-72076 Tuebingen Germany phone: +49-7071-601 401 http://www.eb.tuebingen.mpg.de

Thanks a lot, John! In fact in my base file there were quite a few empty lines that I missed. I changed the basefile and now it works. Best, Georg > I believe that in your base file there was a line with "" for probe > and ACC ids. > Remove the first row of annotation (annotation <- > annotation[2:nrow(annotation),]) and try the code again. > >> Here are the first two lines of the annotation matrix. For reasons >> that >> I do not understand, the first line is empty. Could this be the reason >> for the error? And is there a way to circumvent this? >> >>> annotation[1:2,] >> PROBE ACCNUM LOCUSID UNIGENE >> "" "" "NA" "NA" >> CGENZEB_456000002_0 "CGENZEB_456000002_0" "AF030031" "30131" >> "Dr.30326" >> GENENAME SYMBOL CHR MAP PMID >> GRIF >> "NA" "NA" "NA" "NA" "NA" >> "NA" >> CGENZEB_456000002_0 "deltaA" "dla" "1" "NA" >> "12890499;12835391;12477932" "NA" >> SUMFUNC >> "NA" >> CGENZEB_456000002_0 "NA" >> GO >> "NA" >> CGENZEB_456000002_0 >> "GO:0005509@IEA;GO:0007154@IEA;GO:0009880@IMP;GO:0016020@IEA;GO:000551 >> 5@ >> IDA" >> OMIM REFSEQ >> "NA" "NA" >> CGENZEB_456000002_0 "NA" "NM_130954;NP_571029" >> >> >> Best, >> >> Georg >> >> >>> >>>>> pkgName<-"test" >>>>> pkgPath<-getwd() >>>>> createEmptyDPkg(pkgName, pkgPath, force=TRUE) >>>>> annotation<-as.matrix(annotation) >>> >>> What did annotation contain? Did annotation have column names? You >>> need to >>> provide us with more information (e. g. R version, AnnBuilder >>> version, >>> more >>> example code) >>> >>> >>>> >>>> then I get the following error: >>>> >>>>> writeAnnData2Pkg(annotation, pkgName, pkgPath) >>>> >>>> Error in assign(x[i], value[[i2]], envir = envir, inherits = >>>> inherits) : >>>> attempt to use zero-length variable name >>>> >>>> >>>> Could someone give me a hint what is wrong here? >>>> >>>> Best, >>>> >>>> Georg >>>> >>>> P.S. I am on digest mode, cc'ing the answer directly to me would be >>>> nice >> >> -- Georg Wilhelm Otto Max-Planck-Institute for Developmental Biology Spemannstrasse 35/III D-72076 Tuebingen Germany phone: +49-7071-601 401 http://www.eb.tuebingen.mpg.de