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!
cuffdata <- readCufflinks('/home/sbica1/tophat/finaltrans/tophat/0125diffout')
Creating database /home/sbica1/tophat/finaltrans/tophat/0125diffout/cuffData.db Reading /home/sbica1/tophat/finaltrans/tophat/0125diffout/genes.fpkmtracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading /home/sbica1/tophat/finaltrans/tophat/0125diffout/gene_exp.diff Error in function (classes, fdef, mtable) : unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "integer"
Error in .local(object, x, y, features, ...) : One or more values of 'x' or 'y' are not valid sample names!