CummeRbund Help

[Zapages]

Hi Everyone,

I have small question regarding CummeRbund. Currently, I am getting familiarized with R. Its a very interesting language. Its like an hybrid of Dos and Unix commands from looking at the changing directories and all. All joking aside.

I have taken a look at the gene_exp.diff file and I see that the genes that I am interested are significantly different in expression. The file was viewed through excel.

So the next step I did was download the whole cuffdiff_out folder onto my computer.

I set the folder to cufddif_out folder in R and then ran cummeRbund.

My goal is to show in a nice graphical manner through cummeRbund that these genes of interest (There are about 6 genes) are highly or not being expressed between the two organs. I was thinking of showing a heat map or something along those lines. I am open to any other method as well.

I have followed the cummeRbund manual to no avail.

My Cuff looks like:

CuffSet instance with:
 2 samples
 23228 genes
 27180 isoforms
 26643 TSS
 0 CDS
 22615 promoters
 26643 splicing
 0 relCDS

When I try to look for overall quality:

I get the following errors:

disp<-dispersionPlot(genes(cuff))
Error in sqliteExecStatement(con, statement, bind.data) : 
RS-DBI driver: (error in statement: no such table: geneCount)

When I try to do Step 5: Exploring the data at the gene level on the iPlant's cummeRbund guide. I get errors as well on step 5.3 on doing the sigGenes portion.

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

This tutorial shows for different gene expression, but is there a method to specify what genes in cummerbund?

I found someone who is wanted to do exactly what I am hoping to do. I tried the solution stated in thier question. Unfortunately, it did not work. I was trying this through Atmosphere - RNA-Seq Visualization Instance.

Code solution from: http://www.biostars.org/p/49966/

I got the following error:

myGenes<-getGenes(cuff,MyGeneIds)
Getting gene information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
Error in sqliteExecStatement(con, statement, bind.data) : 
RS-DBI driver: (error in statement: no such table: geneReplicateData)

I tired again on my MacBook Pro with R... I have received this error with different experiment set with 4 samples this time around. I am still having no luck with this.

I used Cufflinks 2.0.2, Cuffmerge2 2.0.2 and Cuffdiff2 2.0.2 to generate the data files. The gene ids are being protected here for research purposes, but the idea is there.

myGeneIds <- c("gene1","gene2","gene3","gene4","gene5")
> myGenes <- getGenes(cuff,myGeneIds)
Getting gene information:
FPKM
Differential Expression Data
Annotation Data
Replicate FPKMs
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: no such table: geneReplicateData)

This is the tutorial: https://insilicodb.org/differential-...ng-cummerbund/

I have been following these tutorials: https://pods.iplantcollaborative.org...A-Seq_tutorial and the CummeRbund manual: http://bioconductor.org/packages/2.1...und-manual.pdf

I would really appreciate any help regarding this. Thank you in advance.

EDIT: Figured it out: I had to rebuild the database file

cuff<-readCufflinks(rebuild=T)