cufflinks diffGenes<-getGenes(cuff,diffGeneIDs) error

[ckrna]

I wish to generate a diff_genes.txt file that includes the XLOC (no problem, includes it now) but also the gene name to make it easier to search for genes of interest.

The workflow breaks down after line 5:

R
library(cummeRbund)
cuff <- readCufflinks()
diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)
diffGenes<-getGenes(cuff,diffGeneIDs)

The last line produces the following error:

Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

The .gtf file is from iGenomes for Homo_sapiens and does include the tss_id and p_id.

May I ask for suggestions to identify the problem and resolve it?

Thanks,
Cris

[lgoff]

Hi, can you please let me know what version of cummerbund you are running. I will try to see if I can reproduce your error...

Cheers,
Loyal

[ckrna]

Hi Loyal,

I have cummeRbund 1.2.0 loaded within R and 1.1.0 loaded external to R.

All help is appreciated. Thanks,
Cris

[mshamblott]

getGenes() problem

I have:
R version 2.15.2
cummeRbund 2.0.0 (loaded feb 6 2013)

1. I am able to do the preliminary data plots but cant get past getGenes(). I'm loading a vector genelist with 2 genes in it

> is.vector(genelist)
[1] TRUE

> print(genelist)
[1] "PROM1" "VAV3"

2. I run getGenes and get this same error.
> Z<-getGenes(cuff,genelist)
Error in sqliteExecStatement(conn, statement, ...) :
RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

I see others have had this problem-PLEASE help!

[lgoff]

Try another call to readCufflinks()

cuff<-readCufflinks()

This will reset the DB connection and you should be good to go.

This problem arises when a previous query has produced an error. I am working to make this less cumbersome of an error.

Cheers,
Loyal

[AgaricX]

Thank you, Loyal! Both for the package and the unparalleled support.

I too was having the 'cannot start a transaction with a transaction' using GetGenes problem, and it was resolved by re-initiating the connection with the database.

Thanks again!

[gwilymh]

I have been getting a very similar error when trying to retrieve gene information.

Input:
geneList<-as.vector(read.table("genesofInterest.txt",sep = "\t",header= FALSE),mode="list")
geneList
geneExp<-getGenes(cuff,geneList)

Output:
Getting gene information:
FPKM
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)

I am working with CummeRbund version 2.0, and (I think) the CuffDiff data was generated with Cufflinks 2.0.2.

I have tried clearing the workspace and reconnecting with CummeRbund; re-downloading all the CuffDiff output files and rebuilding the cuffData.db database; but I still get the same error.

CummeRbund was working fine a few weeks ago with these commands, then abruptly started producing this error message.

Has anyone else had this problem?