Hi all:

I am using CummeRbund and I am in the part when I am preparing the inputs for the statistics about the differentially expressed genes. I used these commands (accord to the manual):

gene.features<-annotation(genes(cuff))

gene.fpkm<-fpkm(genes(cuff))

sample.names<-samples(genes(cuff))

gene.featurenames<-featureNames(genes(cuff))

gene.matrix<-fpkmMatrix(genes(cuff))

gene.rep.matrix<-repFpkmMatrix(genes(cuff))

data(sampleData)

myGeneIds<-sampleIDs

myGeneIds

myGenes<-getGenes(cuff,myGeneIds)

In this point there is an error:

Error in sqliteSendQuery(conn, statement) : 
  rsqlite_query_send: could not execute1: cannot start a transaction within a transaction

Does anyone know how to solve this??? I used this list of commands before and didn't have problems.

Thank you