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:
When I try to look for overall quality:
I get the following errors:
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.
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:
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.
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
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:
Code:
CuffSet instance with: 2 samples 23228 genes 27180 isoforms 26643 TSS 0 CDS 22615 promoters 26643 splicing 0 relCDS
I get the following errors:
Code:
disp<-dispersionPlot(genes(cuff)) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: geneCount)
Code:
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)
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:
Code:
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 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.
Code:
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)
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
Code:
cuff<-readCufflinks(rebuild=T)