Dear Tim, Thanks for your clarifications. I am now trying to either convert existing beadarray generated data into LumiBatch or generate a GEO submittable file from it. But before I embark on a fun if time consuming mission of writing my own code, I would appreciate if you or anybody else could advise me if such functions are already available. Many thanks! Aliaksei. On 03/10/2012 15:56, Tim Triche, Jr. wrote: > yes, you need it to be a LumiBatch or other preprocessing-annotated > object in order for the information to be found > > ExpressionSetIllumina apparently doesn't contain that information. try > running traceback() after you get the error > > > > On Wed, Oct 3, 2012 at 6:59 AM, Aliaksei Holik <salvador at="" bio.bsu.by=""> <mailto:salvador at="" bio.bsu.by="">> wrote: > > Apologies for re-posting this, but I'm concerned that the first > instance got lost. Never again, I promise :) > > > Dear Pan and fellow Biocondictors, > > I am trying to generate a file for submission to GEO database. > However, when trying to generate a Template File I'm confronted by > the following error: > > produceGEOSampleInfoTemplate(__normalised.data, > + lib.mapping=__lumiMouseIDMapping, fileName="GEOTemplate.txt") > The input object should be an object of LumiBatch, MethyLumiM, > matrix or other ExpressionSet inherited class! > Error in templateContent[templateTitle == "Sample_data_processing"] > <- preprocessMethod : > object 'templateContent' not found > > The normalised.data file has been produced using beadarray package > and has the following class: > > class(normalised.data) > [1] "ExpressionSetIllumina" > attr(,"package") > [1] "beadarray" > > I understand, this would qualify it as an ExpressionSet inherited > class and I'm at loss, why it isn't recognised by > produceGEOSampleInfoTemplate. > > I wonder if I should re-code my ExpressionSet as some other class, > and how I might do that. Any help would be much appreciated, > > > Aliaksei. > > P.S. My sessionInfo output and lumi loading messages: > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_2.8.0 nleqslv_1.9.4 methylumi_2.2.0 > BiocInstaller_1.4.7 > [5] ggplot2_0.9.2.1 reshape2_1.2.1 scales_0.2.2 Biobase_2.16.0 > [9] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > Error in x[["Version"]] : subscript out of bounds > In addition: Warning message: > In FUN(c("affy", "affyio", "annotate", "AnnotationDbi", "bigmemory", : > DESCRIPTION file of package 'RSQLite' is missing or broken > > > library(lumi) > Loading required package: methylumi > Loading required package: nleqslv > > bigmemory >= 4.0 is a major revision since 3.1.2; please see package > biganalytics and http://www.bigmemory.org for more information. > > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > > Attaching package: ?lumi? > > The following object(s) are masked from ?package:methylumi?: > > estimateM, getHistory > > Warning messages: > 1: replacing previous import ?image? when loading ?graphics? > 2: package ?nleqslv? was built under R version 2.15.1 > 3: replacing previous import ?density? when loading ?stats? > 4: replacing previous import ?residuals? when loading ?stats? > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > /A model is a lie that helps you see the truth./ > / > / > Howard Skipper > <http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >