Hello everyone, When I try to load my illumina bead summary data into limma i get the following error msg: library(limma) x <- read.ilmn(files="ProbeProfile.txt", ctrlfiles="ControlProbeProfile.txt") Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Canada.1252 [2] LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] limma_3.6.9 loaded via a namespace (and not attached): [1] tools_2.12.0 Any suggestions would be greatly appreciated! Thanks, [[alternative HTML version deleted]]

No worries, it was a problem on my end. All sorted out now, thanks for the quick response! And yes ill definitely look into updating my R thanks :) Kripa Sent from my BlackBerry? smartphone -----Original Message----- From: Wei Shi <shi@wehi.edu.au> Date: Thu, 8 Dec 2011 02:15:00 To: <kripa777 at="" hotmail.com=""> Cc: <bioconductor at="" r-project.org=""> Subject: Re: [BioC] simple limma question (read.ilmn) Dear Kripa, Were you bead summary data from Illumina GenomeStudio/BeadStudio output, or from some other source? The read.ilmn function has been in place for two years and I haven't seen such a problem. BTW, your R is quite old. You should update it to the latest version, although this won't solve your problem. Cheers, Wei On Dec 8, 2011, at 8:49 AM, Kripa R wrote: > > Hello everyone, > When I try to load my illumina bead summary data into limma i get the following error msg: > > library(limma) > > x <- read.ilmn(files="ProbeProfile.txt", > >??????????????? ctrlfiles="ControlProbeProfile.txt") > > Error in dimnames(x) <- dn : >? length of 'dimnames' [1] not equal to array extent > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_Canada.1252 > [2] LC_CTYPE=English_Canada.1252?? > [3] LC_MONETARY=English_Canada.1252 > [4] LC_NUMERIC=C?????????????????? > [5] LC_TIME=English_Canada.1252??? > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets > [6] methods?? base???? > > other attached packages: > [1] limma_3.6.9 > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > Any suggestions would be greatly appreciated! > Thanks, > > >????????????????????????????????????? >??????? [[alternative HTML version deleted]] > > _______________________________________________ > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}

Dear Kripa, Were you bead summary data from Illumina GenomeStudio/BeadStudio output, or from some other source? The read.ilmn function has been in place for two years and I haven't seen such a problem. BTW, your R is quite old. You should update it to the latest version, although this won't solve your problem. Cheers, Wei On Dec 8, 2011, at 8:49 AM, Kripa R wrote: > > Hello everyone, > When I try to load my illumina bead summary data into limma i get the following error msg: > > library(limma) > > x <- read.ilmn(files="ProbeProfile.txt", > > ctrlfiles="ControlProbeProfile.txt") > > Error in dimnames(x) <- dn : > length of 'dimnames' [1] not equal to array extent > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_Canada.1252 > [2] LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets > [6] methods base > > other attached packages: > [1] limma_3.6.9 > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > Any suggestions would be greatly appreciated! > Thanks, > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}