[R] Cummerbund differential expression data analysis package issue

[craigledee]

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!

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