Dear Pan How are you going? I am having some issues with my lumi package as I am unable to create the GEO template despite having the lumi library active. Error: could not find function "produceGEOSampleInfoTemplate" I would appreciate any help from you. Thanks! Cheers Yu

Hi, Yu. Could you please include sessionInfo() and the code that produces the error? Sean On Sat, Sep 10, 2011 at 11:00 PM, Yu Leng Phua <y.phua at="" imb.uq.edu.au=""> wrote: > Dear Pan > > How are you going? I am having some issues with my lumi package as I am > unable to create the GEO template despite having the lumi library active. > Error: could not find function "produceGEOSampleInfoTemplate" > > I would appreciate any help from you. Thanks! > > Cheers > Yu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi, Yu. Your R version and the lumi version are both over 3 years old. I'm not sure that lumi even had the GEO submission stuff in it at that time. In any case, the best plan would be to upgrade to the newest R and lumi and try again. Sean On Mon, Sep 12, 2011 at 9:08 PM, Yu Leng Phua <y.phua at="" imb.uq.edu.au=""> wrote: > Hi Sean > > These are the required information > > R version 2.7.2 (2008-08-25) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australi a.1252 > > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils > ? ?datasets ?methods > [8] base > > other attached packages: > [1] limma_2.14.7 ? ? ? ? lumi_1.6.3 ? ? ? ? ? mgcv_1.4-1 > [4] affy_1.18.2 ? ? ? ? ?preprocessCore_1.2.1 affyio_1.8.1 > [7] Biobase_2.0.1 > > >> produceGEOSampleInfoTemplate(lumi.example, lib.mapping = 'lumiMouseIDMapping', > fileName = "GEOsampleInfo.txt") > Error: could not find function > "produceGEOSampleInfoTemplate" > > > Thanks > Yu > > On Mon, 12 Sep 2011 12:42:37 -0400 > ?Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> Hi, Yu. >> >> Could you please include sessionInfo() and the code that >>produces the error? >> >> Sean >> >> >> On Sat, Sep 10, 2011 at 11:00 PM, Yu Leng Phua >><y.phua at="" imb.uq.edu.au=""> wrote: >>> Dear Pan >>> >>> How are you going? I am having some issues with my lumi >>>package as I am >>> unable to create the GEO template despite having the >>>lumi library active. >>> Error: could not find function >>>"produceGEOSampleInfoTemplate" >>> >>> I would appreciate any help from you. Thanks! >>> >>> Cheers >>> Yu >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >