cummeRbund csHeatmap error

[id0]

I am trying out cummeRbund. Everything seems to be working fine. I tried most of the commands from the tutorial and they all produce reasonable output. However, when I run csHeatmap, I get the following error:

> csHeatmap(genes(cuff))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘csHeatmap’ for signature ‘"CuffData"’

even without any arguments:

> csHeatmap()
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘csHeatmap’ for signature ‘"missing"’

Based on some searching, this does not seem like this is a common issue, so this might be a bug related to my setup. Any idea what could be causing this?

[TiborNagy]

I think this is not a cummeRbund error, but some of the dependecies are missing or outdated.

[id0]

I think this is not a cummeRbund error, but some of the dependecies are missing or outdated.

I tried it on a different machine that I don't use often. It asked me to update outdated dependencies, which I did. Everything should be up to date now. Now I am getting the same error on two very different machines.

[id0]

I went to a clean R 2.14 (more than 2 years old) on a different machine. This installed cummeRbund 1.0.0 (compared to current 2.4.1). Most (if not all) of the dependencies must be different. Still getting the same exact error. How is it possible that I am the only one running into this?

[TiborNagy]

You are not the only one. I also run into this error, but for me the solution was to upgrade one of the dependencies. Do not forget there are dependencies outside R.

[TiborNagy]

Oh, I see what is the problem! You try to visualize CuffData, however csHeatmap is working with CuffGeneSet. To create such datatype you should use getGenes().
Sorry for my previous comment.

[id0]

Oh, I see what is the problem! You try to visualize CuffData, however csHeatmap is working with CuffGeneSet. To create such datatype you should use getGenes().
Sorry for my previous comment.

You're right! That was a huge oversight by me. Nearly every other graphing function takes CuffData, so I didn't notice csHeatmap is different.

Using CuffGeneSet solved the problem. Now I am concerned about clustering. No matter what I put in for that parameter, it seems like the result is poorly clustered. That might be due to the fact that it's graphing FPKMs and not relative expression levels.