Thanks Lynn, It works now. They are two different packages, Wayne -- Lynn Amon wrote: > WG6v2_1.0.zip is not a Bioconductor package. It is just a zip file with > tables of annotated probe information from Illumina. You need to use > biocLite to install the Bioconductor packages. Within R, type: > > source("http://bioconductor.org/biocLite.R") > biocLite("lumiHumanv2") > > Lynn > > > Wayne Xu wrote: > >> Thanks Ann for the response. >> I use illuminaHumanv2, do you mean it differs from lumiHumanv2? >> I download an annotation file from illumina web site, WG6v2_1.0.zip >> I could not install it by command: R CMD INSTALL WG6v2_1.0.zip >> Can you give some hints for this installation? >> >> Thanks again, >> Wayne >> -- >> >> lumiHumanv2 >> >> >> >>> Hello Wayne, >>> As the ls() function showed, there is no illuminaHumanv2TARGETID2NUID >>> function in this annotation package. NUIDs are identifiers invented by >>> the inventors of Lumi. This package only provides annotation from >>> public databases such as NCBI, KEGG, GO and the like. >>> Perhaps, you should try the lumiHumanv2 package. >>> Lynn >>> >>> >>> Wayne Xu wrote: >>> >>> >>> >>>> Hello, >>>> I got following error when I use illuminaHumanv2 annotation package: >>>> >>>> Error in get(x, envir, mode, inherits) : variable >>>> "illuminaHumanv2TARGETID2NUID" of mode "environment" was not found >>>> >>>> >>>> > ls("package:illuminaHumanv2") >>>> [1] "illuminaHumanv2" "illuminaHumanv2ACCNUM" >>>> [3] "illuminaHumanv2CHR" "illuminaHumanv2CHRLENGTHS" >>>> [5] "illuminaHumanv2CHRLOC" "illuminaHumanv2ENTREZID" >>>> [7] "illuminaHumanv2ENZYME" "illuminaHumanv2ENZYME2PROBE" >>>> [9] "illuminaHumanv2GENENAME" "illuminaHumanv2GO" >>>> [11] "illuminaHumanv2GO2ALLPROBES" "illuminaHumanv2GO2PROBE" >>>> [13] "illuminaHumanv2LOCUSID" "illuminaHumanv2MAP" >>>> [15] "illuminaHumanv2MAPCOUNTS" "illuminaHumanv2OMIM" >>>> [17] "illuminaHumanv2ORGANISM" "illuminaHumanv2PATH" >>>> [19] "illuminaHumanv2PATH2PROBE" "illuminaHumanv2PFAM" >>>> [21] "illuminaHumanv2PMID" "illuminaHumanv2PMID2PROBE" >>>> [23] "illuminaHumanv2PROSITE" "illuminaHumanv2QC" >>>> [25] "illuminaHumanv2QCDATA" "illuminaHumanv2REFSEQ" >>>> [27] "illuminaHumanv2SUMFUNC" "illuminaHumanv2SYMBOL" >>>> [29] "illuminaHumanv2UNIGENE" >>>> > lumi.N.ids <- addNuId2lumi(x1.lumi,lib='illuminaHumanv2') >>>> Error in get(x, envir, mode, inherits) : variable >>>> "illuminaHumanv2TARGETID2NUID" of mode "environment" was not found >>>> >>>> I tried >>>> file1 <- '12Probeallprofile.txt' >>>> > x1.lumi<-lumiR(file1, lib='illuminaHumanv2') >>>> I got the same error, >>>> >>>> Thanks in advance >>>> >>>> Wayne >>>> -- >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> >>>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>