Hi Jean, Thanks for running it in your machine. I tried running the same thing in another machine with freshly installed R with bioconductor and got the same error as before. the only difference I see is you have gcrma 2.7.0 while mine is 2.6.0. Will this be the possible cause? I looked at the distribution and found 2.6.0 to be the latest available version. Do you have anything different? Thanks Sucheta My Errors: =========== > affinfo=compute.affinities("soybean") Computing affinities.Done. > myDat <- ReadAffy(filenames="C:/test_bg/49_C033.1B.R9B3L.CEL") > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: soybeanprobe soybeancdf gcrma matchprobes affy affyio "1.14.0" "1.14.0" "2.6.0" "1.6.0" "1.12.1" "1.2.0" Biobase "1.12.2" > tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo) Adjusting for optical effect.Done. Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : variable lengths differ (found for 'x') =================================================== On Tue, November 28, 2006 9:35 pm, Zhijin (Jean) Wu wrote: > Hi, Sucheta, > I got your data and tested it. It runs fine on my machine > > >> affinfo=compute.affinities("soybean") > Computing affinities. > Done. > >> tmp1=bg.adjust.gcrma(myDat,optical.correct=T,affinity.info=affinfo) > Adjusting for optical effect..Done. > Adjusting for non-specific binding..Done. > >> sessionInfo() > R version 2.4.0 alpha (2006-09-06 r39158) > sparc-sun-solaris2.9 > > locale: > C > > > attached base packages: [1] "splines" "tools" "methods" "stats" > "graphics" > "grDevices" > [7] "utils" "datasets" "base" > > > other attached packages: gcrma soybeanprobe matchprobes affy > affyio Biobase > "2.7.0" "1.14.0" "1.5.0" "1.11.6" "1.1.8" > "1.13.2" > soybeancdf "1.14.0" > > > On Mon, 27 Nov 2006, Sucheta Tripathy wrote: > > >> >> Dear List, >> >> >> I still have problem computing background correction with gcrma using >> the following simpler code with soybean chip. >> >> library(affy) library(gcrma) myDat<-ReadAffy() myBG <- >> bg.adjust.gcrma(myDat) >> >> >> My error message is: >> ------------------- >> Adjusting for optical effect.Done. >> Computing affinities.Done. >> Error in model.frame(formula, rownames, variables, varnames, extras, >> extranames, : variable lengths differ (found for 'x') Execution halted >> >> --- >> >> >> my sessioninfo(): ----------------- >> R version 2.4.0 (2006-10-03) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY= en_US >> ;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHO NE=C >> ;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C >> >> >> attached base packages: [1] "methods" "stats" "graphics" >> "grDevices" "utils" "datasets" >> [7] "base" >> ------------------- >> >> >> Has anyone faced similar problem. I am stuck here and any help will be >> greatly appreciated. This seemed to work well with the earlier versions >> of R and soybeancdf. >> >> >> Many thanks >> >> >> Sucheta >> >> >> >> >> >> >> >> -- >> Sucheta Tripathy, Ph.D. >> Virginia Bioinformatics Institute Phase-I >> Washington street. >> Virginia Tech. >> Blacksburg,VA 24061-0447 >> phone:(540)231-8138 >> Fax: (540) 231-2606 >> >> >> web page: http://staff.vbi.vt.edu/sutripa blog : >> http://genomics-array.blogspot.com/ >> >> >> _______________________________________________ >> 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 >> >> > -- Sucheta Tripathy, Ph.D. Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 web page: http://staff.vbi.vt.edu/sutripa blog : http://genomics-array.blogspot.com/