Can cummeRbund analyze the output of running cufflinks?

[jerryeah]

Can cummeRbund analyze the output of running cufflinks?
Since in the manul of cummeRbund, there is a sentence like this:

CummeRbund was designed to help simplify the analysis and exploration portion of RNA-Seq data derrived from the output of a differential expression analysis using cuffdiff with the goal of providing fast and intuitive access to your results.

And when I try to use it to analyze my result, an error is given:
> cuff<-readCufflinks(rebuild=T)
Creating database /home/jerry/graduation_project/result/UHR100_cuff/cuffData.db
Reading /home/jerry/graduation_project/result/UHR100_cuff/genes.fpkm_tracking
Checking samples table...
Populating samples table...
错误于data.frame(index = c(1:length(samples)), sample_name = samples) :
arguments imply differing number of rows: 2, 0


So I really not certain about that?
Any one can help? Thanks a lot

[sdriscoll]

it is intended to run on the output of cuffdiff - the differential expression tool packaged with cufflinks.

[jerryeah]

But in the Q&A of cufflinks,http://cufflinks.cbcb.umd.edu/faq.html#visi

there is a conversation like this:
How can I visualize by Cufflinks and Cuffdiff results?
We've built CummeRbund for this purpose, which is based on the elegant, powerful ggplot2 library for this. It's written by Hadley Wickham in R and makes plotting very simple.

So i am really perplexed.

[Q.Zhang]

see:http://www.nature.com/nprot/journal/....2012.016.html

You may find the useful information for your purpose.

[sdriscoll]

Also see: http://compbio.mit.edu/cummeRbund/manual.html#tth_sEc4. They say it there that it was designed for cuffdiff output.

[jerryeah]

Also see: http://compbio.mit.edu/cummeRbund/manual.html#tth_sEc4. They say it there that it was designed for cuffdiff output.

Okay, it seems you are right. I am trying to figure out some other methods. Thanks a lot : )

[jerryeah]

see:http://www.nature.com/nprot/journal/....2012.016.html

You may find the useful information for your purpose.

Thanks for your information. Since the cummeRbund package can't process the output of running cufflinks, I am trying to write some scripts to analyse it.

[jp.]

if you get diff_out results, you can analyse using cummeRbund
reply if you have problem... I solved the problem..