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Old 03-06-2014, 03:08 PM   #1
Location: NJ

Join Date: Oct 2012
Posts: 94
Default CummeRbund getGenes command broken in R?

Hi Everyone,

I don't know what exactly happened. I have been working with R and cummeRbund for the past few months. Everything seemed to be fine with the

getGenes command in the manual.

Apparently, when I enter the getGenes commands. I get the following error:

> myGenes <- getGenes(cuff,myGeneIds)
Getting gene information:
Error in sqliteExecStatement(con, statement, : 
  RS-DBI driver: (error in statement: near ")": syntax error)
I am using latest version of cummeRbund with R. Also my Cuffdiff output was done through Cufflinks/Cuffmerge/Cuffdiff 2.0.2.

I checked my old data, which has worked in the past and I received the same error, which is strange.

Also I have reinstalled cummeRbund as well. I've rebuilt the database file as well. No matter, what I do I get this same error.

If someone could kindly help me. I would really appreciate it.

Thank you,


Last edited by Zapages; 03-06-2014 at 03:17 PM.
Zapages is offline   Reply With Quote
Old 03-07-2014, 04:28 AM   #2
Senior Member
Location: Budapest

Join Date: Mar 2010
Posts: 329

Maybe the problem is not in CummerRbund, but in the SQLite server or client.
TiborNagy is offline   Reply With Quote
Old 09-10-2014, 12:56 PM   #3
Location: Irvine CA, USA

Join Date: Dec 2009
Posts: 29

Regardless of where the problem lies it renders many of my needs unattainable and removes a lot of cummeRbund's function.

Has anyone found a way to get past this yet?

I have tried rebuilding the database with

But it breaks again as soon as I try to repeat

my_sig_genes = getGenes(cuff, my_sig_gene_ids)

In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
--Stephen Jay Gould
Gus is offline   Reply With Quote

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