An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070903/ 24ce1138/attachment.pl

Hi Alessandro -- I think this is a limitation of buildChromLocation. Most annotation packages (e.g., hgu95av2) have a 'map' between probe names and the corresponding gene SYMBOL identifiers. The yeast community has gone a different route, and uses GENENAME identifiers: the yeast packages have yeast2GENENAME maps, rather than yeast2SYMBOL. To get around this, I think you will need to create a copy of buildChromLocation, e.g., by using the output of > buildChromLocation to define a function buildYeastChromLocation. Then edit the line near the end to replace "SYMBOL" with "GENENAME". Likely other parts of the package make similar kinds of assumptions. Hope that helps, Martin Alessandro Fazio <fazioalessandro at="" hotmail.com=""> writes: > Hello everybody, > > I have been trying to assemble a chromLocation object by following the code in the vugnette of geneplotter package. > > BUT, at the end I got this error message: > >> newChrClass <- buildChromLocation("yeast2")Error in get(x, envir, mode, inherits) : variable "yeast2SYMBOL" was not found > Even if the yeast2 package is loaded, the variable yeast2SYMBOL is not found. > > Any idea to help me? > > Thank you very much in advance > > Alessandro Fazio > >> sessionInfo()R version 2.5.0 (2007-04-23) 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] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" > other attached packages: ygs98 hgu95av2 yeast2 geneplotter lattice annotate Biobase "1.16.0" "1.16.0" "1.16.0" "1.14.0" "0.15-4" "1.14.1" "1.14.0" > _________________________________________________________________ > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org