R help - Apr 2012 - Cummerbund differential expression data analysis package issue

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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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!
>
> --
> 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.
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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