On 04/17/2012 10:02 AM, craigledee wrote:
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!
Hi cRaig
cummeRbund is a Bioconductor package so ask on the Bioconductor mailing list
http://bioconductor.org/help/mailing-list/#bioconductor
(without subscribing via
http://bioconductor.org/help/mailing-list/mailform/ if that's more
convenient)
Be sure to include the package maintainer
packageDescription("cummeRbund")$Maintainer
in the email.
Martin
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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