Help with cummeRbund

[Name_less_]

Hello
I am new in R, but I am work with cummeRbund.
I followed the next steps:

> library(cummeRbund)
> cuff_data < - readCufflinks("diff_out")
> csDensity(genes(cuff_data))
> csScatter(genes(cuff_data), "X571A", "X57B", "X571C", "X571D" )

BUT, I have the next error:

Error en if (logMode) { : argumento no interpetable como lógico

Someone can help me please?

I have four conditions without replicates.

[blakeoft]

Is it giving you that error just for the csScatter() call? What does it say if you just type "csScatter" with no arguments or parentheses? It looks like it's saying that logMode isn't a logical parameter, but it's definitely set to T by default.

[Name_less_]

No, I have similar error with csVolcano. I followed the steps of the TOPHAT paper (Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, nature protocols).

[blakeoft]

Does that error message mean something like "argument not interpretable as logical"?

Also, could you tell me what "csScatter" prints to your screen?

When I type that, I see

> csScatter
standardGeneric for "csScatter" defined from package "cummeRbund"

function (object, x, y, logMode = TRUE, pseudocount = 1, labels,
    smooth = FALSE, ...)
standardGeneric("csScatter")
<environment: 0x12289cc4>
Methods may be defined for arguments: object, x, y, logMode, pseudocount, labels, smooth
Use  showMethods("csScatter")  for currently available ones.

In particular, it says "logMode = TRUE". Thus logMode is interpretable as logical because it is by default. Does your say "logMode =" with something other than "TRUE", or whatever the Spanish version of TRUE in R is?

[Name_less_]

This is what the csScatter prints in my screen:

> csDensity(genes(cuff_data))
Mensajes de aviso perdidos
1: Removed 6 rows containing non-finite values (stat_density).
2: Removed 3 rows containing non-finite values (stat_density).
3: Removed 8 rows containing non-finite values (stat_density).
4: Removed 4 rows containing non-finite values (stat_density).
> csScatter(genes(cuff_data), "X571A","X571B","X571C","X571D")
Error en if (logMode) { : argumento no interpetable como lógico

In the previous step, I have not problem (in csDensity)

And when I type csScatter, I obtain this:

> csScatter
standardGeneric for "csScatter" defined from package "cummeRbund"

function (object, x, y, logMode = TRUE, pseudocount = 1, labels,
smooth = FALSE, ...)
standardGeneric("csScatter")
<environment: 0xe001228>
Methods may be defined for arguments: object, x, y, logMode, pseudocount, labels, smooth
Use showMethods("csScatter") for currently available ones.

[blakeoft]

Oh, I think I see what's going on. I don't know why I didn't see it before. Are "X571A", "X571B", "X571C", and "X571D" your conditions? csScatter() is seeing genes(cuff_data) as the object argument, "X571A" as the x argument, "X571B" as y and "X571C" as logMode. But "X571C" obviously isn't a logical value, so it gives you an error.

It looks as though you can only plot two samples at a time, which makes sense because you only have two axes. You could do the six pairwise comparisons I guess. Maybe csScatterMatrix is what you want, I just don't have experience with it so I don't know for sure. So something like

csScatter(genes(cuff_data), "X571A", "X571B")

should work. Post back if it still gives you issues.

I'm sorry it took so long for me to realize what was happening. I thought it was a (human spoken) language issue at first.

[Name_less_]

Sorry for the late but I was full work.
Thanks for all. That was the solution. Thanks!!! Now I can create the graphics needed.
THANKS!! jeje
Greetings!