Hi all, I'm having the same issue as in this previous post: http://r.789695.n4.nabble.com/R-error-td4200447.html#a4209042
And as another user of Biostar: http://www.biostars.org/post/show/42562/cummerbund-isnt-managing-cuffdiff-database/#42895 Whereby I'm trying to output cuffdiff data into cummeRbund, but it appears to be having issues with connection to a database (below). Does anyone have any suggestions as to how I can fix this? Thanks! cuff_data <- readCufflinks('/home/sbica1/tophat/finaltrans/tophat/0125diff_out') Creating database /home/sbica1/tophat/finaltrans/tophat/0125diff_out/cuffData.db Reading /home/sbica1/tophat/finaltrans/tophat/0125diff_out/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing gene Data table Reading /home/sbica1/tophat/finaltrans/tophat/0125diff_out/gene_exp.diff Error in function (classes, fdef, mtable) : unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "integer" csVolcano(genes(cuff_data),'0',36) Error in .local(object, x, y, features, ...) : One or more values of 'x' or 'y' are not valid sample names! -- View this message in context: http://r.789695.n4.nabble.com/Cummerbund-differential-expression-data-analysis-package-issue-tp4565409p4565409.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
