Hi there, I have a problem in using cummeRbund and the issue is similar with the thread http://seqanswers.com/forums/showthread.php?t=18830 but not the same. Hope anyone can help me to solve this question..
I use the R(2.15.0) and cummeRbund 1.2.0.
IMO there should be something wrong(format?) in my gene_exp.diff so the RSQLite package aborted. And the cuffData.db do built up but I'm wondering if it is complete..
Hope for your reply. Thanks ^_^
I use the R(2.15.0) and cummeRbund 1.2.0.
Code:
> library(cummeRbund) Loading required package: RSQLite Loading required package: DBI Loading required package: ggplot2 Loading required package: reshape2 > cuff<-readCufflinks("cuffdata_120417") Creating database cuffdata_120417/cuffData.db Reading cuffdata_120417/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Reading cuffdata_120417/gene_exp.diff Error in function (classes, fdef, mtable) : unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical" >
Hope for your reply. Thanks ^_^
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