cummeRbund Create Gene Set Error

Question

I am having trouble creating a Gene Set using cummeRbund (R software used to analyze cufflinks, cuffdiff output).

I have been working from the cummeRbund manual that can be found here The directions have worked up until the point of creating the gene sets.

Before creating the gene sets you need to create a vector of gene_ids to include. In the example they enclose each item in this list in quotation marks. I have a created a gene_ids .txt file named OtoSCOPE_v7_list_oneline.txt the first 4 entries in this list are shown below.

“Adcy1” “Bdp1” “Bsnd” “Cabp2”

Here is the create gene sets portion of the script that I have been using.

###################################
# Creating Gene Sets
###################################
#first created a vector of gene_ids that you want included in your gene set
base_dir <- "/Users/paulranum/Documents/cummeRbund"
otoscope_genes <- read.table(file.path(base_dir, "OtoSCOPE_v7_list_oneline.txt"), stringsAsFactors=FALSE)

data(cuff)
myGeneIds<-otoscope_genes
myGeneIds
myGenes<-getGenes(cuff, myGeneIds)
myGenes

When I run this I get the following output and errors.

> data(cuff)
Warning message:
In data(cuff) : data set 'cuff' not found
> myGeneIds<-otoscope_genes
> myGeneIds
       V1     V2     V3      V4      
1 “Adcy1” “Bdp1” “Bsnd” “Cabp2” 
> myGenes<-getGenes(cuff, myGeneIds)
Error in rsqlite_send_query(conn@ptr, statement) : 
  cannot start a transaction within a transaction
> myGenes
Error: object 'myGenes' not found

From what I can tell there are two main issues going on.

1. it is not recognizing my data(cuff) command. cuff is the name of my CuffSet data file this file has worked for everything else. is this not the correct data file?
2. the error after the myGenes<-getGenes(cuff, myGeneIds) command:

Error in rsqlite_send_query(conn@ptr, statement) : cannot start a transaction within a transaction

Thanks for reading any help would be very much appreciated.